Month: January 2009

Vaccine Safety: A Debate

Seth Roberts9 Comments

As I said on Christmas Eve, thanks to Web comments and blogs, you can now hear many voices in a debate in a way you never could before. The New York Times has just added a vote-like recommendation feature to help sift through a large number of comments. (I hope they add a “sort by” feature to make the most popular comments easy to find.) People you could not usually hear from turn out to have enormously interesting and helpful things to say — again and again and again.

A new example is the debate over vaccine safety. A 2007 book called The Vaccine Book: Making the Right Decision For Your Child by Robert Sears took a middle ground: A way that parents can space out vaccines. This seems to have offended Dr. Paul Offit, a vaccine inventor. With Charlotte Moser he wrote a critique (may be gated) of the book, just published in Pediatrics, that is actually an attack on it. Would the critique be full of well-reasoned arguments? New facts? Nope. It reminds me of my surgeon claiming that a certain surgery was beneficial and, when questioned, saying that of course evidence supported her claim but never producing any evidence. However, overstatement from doctors is nothing new. What’s new is the comments section on the critique (may be gated), which contains several fascinating observations.

From John Trainer, a family doctor:

[For Offit and Moser] to castigate [Sears] for offering information to the laity is to fall prey to the same mindset as the early church. By controlling access to the Bible, the leaders of the church exerted control over all.

From Corrinne Zoli, a Syracuse University researcher:

The vaccine debate plays out against a backdrop not only of facts vs. falsehoods, refereed vs. non- mainstream journals and studies, science vs. speculation, a complicated enough arena, but of conflicting cultural ’facts,’ which may be equally important as the science. For instance, parental concerns over the safe cumulative levels of thimerosal (ethyl mercury) in vaccines were unwittingly validated by the American Academy of Pediatrics (AAP) and the U.S. Public Health Service and others’ recommending their removal (which largely occurred in 2001)—even while these organizations were steadfast in public declarations of no causal link between the preservative and various neurotoxic or neuropathological ill-effects. What did parents learn from this decision? Aside from the fact that the preservative had been long removed in many countries of the world (i.e., the UK and even Russia), or that infants may have received doses exceeding EPA recommendations, they learned that organizations designed to serve the public trust were contradictory in their words and deeds. . . . The larger ’lesson learned’ by parents was to fear the decision making processes of medical and public health institutions and to become critically engaged with them using whatever tools at one’s disposal (i.e., online information, reading scientific studies, discussion groups, etc.).

Fifty years ago, when doctors wouldn’t justify their claims, you couldn’t do much about it. Few had access to medical libraries or the time to visit them. Now there is an enormous amount you can do. Water will simply flow around the rocks, such as Dr. Offit, who get in the way of better decisions.

This sort of open discussion is so helpful it should be standard scientific practice: allow your research to be commented on by anyone for anyone to read.

Beijing Shopping (the Beijing Zoo)

Seth Roberts2 Comments

A Beijing friend of mine prefers to shop in Hong Kong, where clothes are cheaper than in Beijing. If you must shop for clothes in Beijing, she said, go to the Beijing Zoo. She meant a cluster of stores near the zoo.

When the movie Titanic came out, and I knew it cost a lot to make, I thought I’d lose money if I didn’t buy a ticket to see it. For the first time since Titanic I had a similar feeling: At the Beijing Zoo prices were so low it felt like losing money if I didn’t buy something.

On seven floors there were hundreds of shops, each crammed with some clothing item: dresses, scarves, shoes, jackets, pants, shirts, and so on. More shoes than anything else. (Few socks.) I wanted to buy shirts but the shirt selection was poor, consistent with the fact that the shirts I already have are from Malaysia, the Philippines, and Hong Kong. But because I could buy a $6 shirt that would cost $80 in America, I bought a few anyway. I was happier with the shoes I bought ($10 here, $100 in America).

I love shopping (but alas dislike owning) and especially love Chinese shopping because the sticker price is often just a starting point. It is like adding spices to food. At the first shoe vendor, the quoted price for shoes I liked was $40. I got up to leave. What’s your lowest price? I asked. $30. I started to leave. What’s your price? she asked. What’s your lowest price? I repeated. As I left, the price went down to $20. That’s your lowest price? I asked. Yes, she said, what’s your price? That was helpful. With other vendors, I started at $7 and gradually increased my offers to $10, at which point they were accepted — but only if I was leaving. Sometimes the sticker price was the actual price. For a jacket advertised at about $14 I paid about $14, even though another stall a few feet away had the same thing. I went back and forth between the vendors and $14Â was the best I could do.

I hoped to buy a winter jacket but to my astonishment couldn’t find one I liked. The student store at Tsinghua has about five winter jackets for sale and I would happily buy one of them ($50). Among hundreds and hundreds of men’s winter jackets at Beijing Zoo I didn’t see a single one I liked. Good excuse to return . . .

The Shangri-La Diet Hedonic Shift

Seth Roberts5 Comments

On the SLD forums, Bennetta wrote:

I never noticed this before, but I used to eat as a way to thwart boredom. Nothing to do? Make some food! The odd thing here is finding myself doing a ton of other things when I would have otherwise been cooking or eating just to entertain myself. Now, instead of heading to the fridge when there’s nothing to do, I clean, write letters to friends, or do whatever.

This change in behavior shows that the Shangri-La Diet makes food less pleasant. When we don’t feel good (such as are bored), we look around for activities that will make us feel better. Eating is no longer one of those activities. This shift in the hedonic value of food — which happens because our set point becomes lower than our weight — painlessly keeps us from eating. Or if we do eat, we stop sooner.

Michel Cabanac, a professor of physiology at Laval University, Quebec City, has studied how hedonic shifts control behavior in several areas, including thermoregulation and body weight regulation.

A Statistics Package in the News

Seth Roberts7 Comments

I use R, the open-source version of S, several times/day. More often than I use Word. It works far better than S — fewer bugs, much cheaper (R is free) — and S worked a lot better than what it replaced (STATGRAPHICS). I was pleased to see a NY Times article about it:

R has also quickly found a following because statisticians, engineers and scientists without computer programming skills find it easy to use.

“Easy to use” — haha! Non-statisticians and non-engineers don’t find it easy to use, in my experience, but it’s true that I found it easy to use. “R has a steep learning curve” some people say, twisting the meaning of “steep learning curve” (which should mean fast learning, since that’s what a steep learning curve describes).

The popularity of R at universities could threaten SAS Institute, the privately held business software company that specializes in data analysis software. SAS, with more than $2 billion in annual revenue, has been the preferred tool of scholars and corporate managers. . .SAS says it has noticed R’s rising popularity at universities, despite educational discounts on its own software, but it dismisses the technology as being of interest to a limited set of people working on very hard tasks.“I think it addresses a niche market for high-end data analysts that want free, readily available code,” said Anne H. Milley, director of technology product marketing at SAS. She adds, “We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.”

Ah, “freeware.” You may remember when “Made in Japan” was derogatory. Most psychology departments, including Berkeley, use SPSS (Statistical Package for the Social Sciences). Like SAS and its ten feet of manuals, it is horrible. One of my students wanted to make a scatterplot of her data. She went to the psych departmental statistics consultant (a psych grad student who had taken courses in the statistics department). The statistics consultant didn’t know how to do this! A scatterplot! It’s like Vladimir Nabokov’s observation at Cornell and other schools of language professors who couldn’t speak the language they taught. Nothing But the Best describes a Julliard composition teacher who couldn’t read music. To be a scientist and not be able to analyze your own data is pretty much the same thing. With R making a scatterplot is easy.

To me, the value of R is that it makes high-quality data analysis available to everyone — something very new in the history of mankind. R makes self-experimentation easier because it makes data analysis easier and allows you to learn more from the data you have collected (e.g., make better graphs). I also use it for data collection — measuring how well my brain is working.

Via Andrew Gelman.

Kafkaesque Research Regulation

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From the BMJ:

The local research ethics subcommittee, which comprised a pharmacist and layman with limited clinical experience, had concerns about possible drug interactions between amiloride and other drugs being taken by the study participants and hyperkalaemia and requested resubmission. Although we pointed out that the pilot was identical to one limb of the amendment that it had already approved, in September 2007 the full committee rejected the application for the pilot to be considered as a study amendment. We therefore had to make new submissions to the local ethics committee, Medicines and Healthcare Products Regulatory Agency (MHRA), pharmacy, insurance company, research and development department, and the local (Wellcome Trust) clinical research facility.

In Spain it takes years to get approval. By the time you get approval someone else has published the study you wanted to do. A nightmarish research environment is one more reason that persons with health problems should do their own research: try to find solutions themselves. I started long-term self-experimentation because I knew that conventional sleep research would never — at least, in my lifetime — help me understand why I often woke up too early. A common problem, easy to measure — but conventional sleep research is nearly impossible.

Can it get worse? Yes, in Russia.

Lipid Values after 2 Years on the Shangri-La Diet

Seth Roberts6 Comments

Stephen Marsh has been doing the Shangri-La Diet for 2 years, taking about 6 tablespoons of ELOO (extra light olive oil) per day. He recently got an expanded set of blood tests done. Here are the results. (10-90%ile mean 10% and 90% percentiles in the general population):

  • LDL IIIa+b (%). 10-90%ile 13.6 — 43.0; Alert Value >20; SM = 17
  • LDL IVb. 10-90%ile 1.7-9.8; Alert Value >10; SM = .9
  • HDL2b (%). 10-90%ile 7-30; Alert Value <10; SM = 29
  • Apo B. 10-90%ile 60-140; Alert Value >120; SM = 48
  • Lp(a). 10-90%ile 0-30; Alert Value >30; SM = 10
  • Lp_PLA2. 10-90%ile 155-419; Alert Value >223; SM = 197
  • Insulin. 10-90%ile 3-25; Alert Value 12; SM = 9
  • NT-proBNP. 10-90%ile 5-125; Alert Value 450; SM = 14
  • Cholesterol       134
  • Triglycerides     51
  • HDLÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 67
  • LDLÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 57
  • Glucose           86

Stephen added:

Two years after the weight loss, taking in what so many of these “experts” say is a dangerous level of fat as a dietary supplement, my bloodwork, especially the important markers, is very good. Bottom line is a low level of small LDL particles and a miniscule level of the dense, dangerous ones (below the reference range). On the HDL (the “bad” cholesterol) the particles are about half of the largest or non-dangerous kind.

Tracking How Well My Brain is Working

Seth Roberts5 Comments

From my omega-3 results I got the idea that our brains may work better or worse without our noticing. I want to track how well my brain works not only to test the effects of different dietary fats (our brain is more than half fat) but also to allow the possibility of discovering new effects, both good and bad.

One test I am using is a typing test (early results here). Another is an arithmetic test. I got the idea of using arithmetic from Tim Lundeen. Like him, I found that the speed with which I could do simple arithmetic problems (8+0, 4*3) was sensitive to the amount of omega-3 in my diet.

The arithmetic test involves doing 100 problems separated into 5 blocks of 20 each. There is little time between each problem. I type the last digit in the answer; e.g., if I see 8*8 I type 4. The possible answers are 1, 2, 3, 4, 7, 8, 9, and 0 so that I don’t have to move my fingers off the keys. There is feedback after each block. I aim for 95% correct.

This is my second use of an arithmetic test. The advantages of this one compared to several other tasks I have tried are:

  • Portable. Only requires a laptop.
  • Well-learned. So I should plateau (reach a steady speed) sooner than with a task I learn from scratch. When my speed is steady it will be easier to compare different conditions — no need to correct for learning.
  • Uses eight fingers. Many tasks used by experimental psychologists have just two possible answers (yes/no). With eight possible answers there is less anticipation and less worry about repetitive strain injury.
  • No data entry. The task is written in R, the language I use to analyze the data.
  • Many measurements per minute. This allows me to correct for problem difficulty and get a standard error for each test session.

Here are early results.

In the test sessions after January 1, two sets of points are above the line — I was slower than expected, in other words. Both came from test sessions about an hour or so after I woke up. At the time of those sessions I felt fine — not tired, not groggy — and was a little surprised. This is a trivial example of what I am looking for: new environmental effects.

The bigger context of this research is that scientists know a lot about idea testing but almost nothing about idea generation — how to find new ideas worth testing. Maybe this research will teach me something about idea generation.

A talk by Tim Lundeen about related stuff.

Things That Work Much Better When Broken (part 2)

Seth Roberts2 Comments

If six months ago you had told me such things existed I would have been very skeptical. But since then I have come across two examples. Example 1: contact lenses. Forced during a trip to wear just one lens (leaving one eye without a lens), I realized my sight was much better than when I wore two. I had sharp vision both close and far away. And the unlensed eye got more oxygen than usual.

Example 2 I also discovered by accident. My bike lock no longer locks. It is hard to see this, so if I fake-lock my bike — which I got for free — it is still sufficiently protected. My bike lock is now much easier to use. No more worry about the key. No way it can become impossible to unlock, which has happened once in two months. (To any Tsinghua students reading this: Please don’t steal my bike.)