Seth's Blog

An account of the genomics scandal at Duke University has appeared in Significance (a journal sponsored by British and American statistical societies). The scandal caused the end of a clinical trial — it had been based on fraudulent data — and the resignation of assistant professor Anil Potti, who had among other things falsified his resume.

It reminded me of the Ranjit Chandra case. Similarities: 1. The published results could not be reconstructed from data. In Chandra’s case, some of the results were statistically impossible. In the Potti case, two statisticians were unable to go from raw data they were given to the published results. 2. Outsiders important. Saul Sternberg and I, who are psychology professors, not nutrition professors, wrote an article that drew attention to what Chandra had done and caused retraction of one of his papers. As far as I could tell, at least a few nutrition professors had believed for many years that Chandra made up data. In Potti’s case, the deception was revealed by two statisticians. Perhaps Chandra and Potti both believed (a) hardly anyone will notice and  (b) if anyone notices, they won’t do anything. 3. Incidental fabrication. In one paper, Chandra said that everyone asked to be in the study agreed to participate. The study involved having blood drawn many times. Potti claimed to be something similar to a Rhodes Scholar. 4. Found innocent. Years before Sternberg and I got involved, Chandra had been accused by his research assistant, a nurse. A Memorial University committee found him innocent of her accusations — at least, her accusations were not upheld. Chandra then sued the nurse. In the Potti case, a Duke University committee looked into the case and found no serious wrongdoing. A clinical trial based on the Potti results, which had been stopped, was resumed.

Factor 2 (outsiders important) is no surprise to readers of this blog, although the new account doesn’t mention it. But Factors 1 (reconstruction impossible) and 3 (incidental fabrication) mean that the fabrication should have been relatively easy to confirm. Yet Factor 4 seems to suggest it was hard to confirm. Factor 4 — in spite of Factors 1 and 3 — implies there is something mysterious and important going on here, more mysterious and interesting than someone lying. But I cannot say what.

The Significance article, which is by Darrel Ince, a professor of computing at the Open University, includes several suggestions for improving the system. I fail to see why they will help and they have significant costs. One of them is to put the original data and software in an independent repository. I think this would make things worse. People would continue to fake research; now. they would now also fake raw data, in addition to the graphs and tables needed for publication. In the past, thinking they wouldn’t be caught, fakers would either (a) not make up the raw data (Chandra) or (b) do so carelessly (Potti). Their overconfidence was key to catching them.

My suggestion along these lines is a requirement that researchers make available upon request the raw data and any original software. They store it themselves, in other words. If they fail to fulfill outside requests for these materials within one month, this will be grounds for immediate retraction of the paper. Without something like this, a store-it-yourself requirement means little. I once requested the raw data for a paper that had appeared in a journal that had a make-data-available policy. The authors refused my request. The editor did nothing. As A. W. Montford makes clear in The Hockey Stick Illusion, we would all be better off if Michael Mann and other authors had simply handed over the raw data behind their “hockey stick” temperature graphs when requested rather than fight a long string of FOIA battles (and mull over what emails to delete).

With the ability to measure individual genes has come interest in learning what they do. Perhaps Person X is depressed and Person Y is not depressed because Person X’s genes differ from Person Y’s. A whole generation of psychiatry researchers now believes this is plausible. There are “general reasons to expect that GxEs [gene by environment interactions] are common,” says a new review paper in the American Journal of Psychiatry. By “common” they mean large enough and common enough to do research about. (more…)

• more evidence that chocolate is healthy. “The highest levels of chocolate consumption were associated with a 37% reduction in cardiovascular disease and a 29% reduction in stroke.” This is good news.
• The great bank robbery by Nassim Taleb and Mark Spitznagel. “For the American economy . . . the elephant in the room is the amount of money paid to bankers over the last five years.. . .  That $5 trillion dollars is not money invested in building roads, schools and other long-term projects, but is directly transferred from the American economy to the personal accounts of bank executives and employees. Such transfers represent as cunning a tax on everyone else as one can imagine.” This is a new variation of “behind every great fortune is a great crime”.
• Nutritionist, heal thyself. Fat is obviously good for the skin. Which suggests it is good for the whole body, just less obviously.
• The Taleb/Spitznagel point is supported by this article (via Marginal Revolution), which concludes: “Who has been the first to lose confidence in the European banking system? . . . The European banking system itself.” As they say: Don’t con a conner.

Standing desks are becoming popular. From a WSJ article:

A growing number of workers at Google Inc., Facebook Inc. and other employers are trading in their sit-down desks for standing ones, saying they feel more comfortable and energized. They also are motivated by medical reports saying that sitting for too long leads to increased health risks.

I started standing while working fifteen years ago, after I found that I slept better if I stood a lot. I got a standing desk. (Parts at Ikea $100.) I made what was apparently the first treadmill desk. But since then I learned a lot and my preferences changed. I never went back to a conventional desk, but I found that a standing desk wasn’t optimal. Here’s what I learned:

1. Standing a lot is not all good. Standing in one place for a long time is psychologically difficult. If I stood for more than 8 hours or so, my feet started to hurt. Yet I needed at least 8 hours of standing to get the sleep benefits. I also found epidemiology that suggested that if you stand a lot, your blood puddles in your legs, with bad effects. Above all, standing in one place is distracting, probably because it is inherently unpleasant. I find it much easier to write in the lounge-like position I describe below.

2. Walking a lot is bad. I work perhaps 8 hours per day. No way would I walk that much. The main use of my treadmill desk was standing, not walking. There was also a noise problem. Occupants of adjacent office complained.

3. Walking a little is good. If I walk about 20 minutes per hour, I found I can work really long periods of time–without stimulants. I have also found that walking makes my brain work better. The measure I used to detect this improvement was arithmetic speed but I’m sure it applies to all sorts of thinking.

4. One-legged standing can produce the sleep benefits of normal standing. The benefits of better sleep are huge. After I started sleeping better, mainly because of standing a lot, I stopped getting obvious colds. I also felt more energetic during the day.

When you put these together it is easy to grasp that the best workplace will not involve, as its main component, a standing desk.

Nowadays I mix lounge-like sitting (there is no one word for it) and walking. By “lounge-like sitting” I mean I sit in such a way that I lean back somewhat (so that some of my weight is on my back) and my knees are both bent and supported. The chair pictured above is the closest piece of furniture I could find designed for this. The goal of such a piece of furniture is to make the surface area (i.e., skin) supporting you as wide as possible so that the maximum pressure is minimized. A normal chair does a terrible job of this, but even the chair in the picture is not ideal: (a) It should have armrests. (b) It should have adjustable weights so that the angle at which it reclines can be set to the best position. How much walking I do depends on the time of day. During the day, when I feel restless, I might walk on a treadmill 20 minutes per hour. In the early morning and evening I don’t walk at all.

It’s fascinating there’s no word for an action I spend many hours every day performing and that perhaps a billion people would do many hours per day if they could. (At least a billion people have jobs where they must sit in ordinary chairs.) What I do is roughly a billion times more comfortable. Given the size of the market and the size of the benefit, it is equally fascinating that you cannot buy anywhere the proper furniture for doing this. The company that made the chair in the picture seems to have stopped making it. This should give pause to anyone who thinks that any or all of (a) free markets, (b) governments, or (c) academic/pure research can produce all the products we need to live a healthy happy life.

A colleague I’ll call John has decided to start tracking his mood for a long period of time (years). He explains why:

A few years ago, after a severe manic attack, I was diagnosed with bipolar disorder. The attack was preceded by an intense period of stress, then two weeks of elevated mood, increased social activity (hanging out and meeting people), and racing thoughts (hypomania). Then I skipped a few nights of sleep, wandered down roads in the middle of the night, and eventually became psychotic, in that I could no longer distinguish between reality and imagination. I was chased by cops on several occasions, and was involuntarily committed to the mental health wing of a hospital for a month. It put a massive dent in my life.

Family, medicine, and time helped me recover. Being out of control like that was fun only for the first two weeks. Having my life turned upside down was not fun either. As I recovered I became increasingly interested in finding ways to prevent a relapse. One doctor said: You have a vulnerability. You need to protect yourself. I agreed.

Looking back on the experience, I realized there was a rise in odd behaviors two weeks before I started to skip nights of sleep and fell into psychosis. There was an even longer buildup of stress, anxiety, and fear in the months before the mania hit. During the last two weeks before the mania, my behavior was different from what is normal for me. I felt elated and had a sense of general “breakthrough”. I suddenly felt no fear and anxiety. I felt on top of the world. I was constantly taking notes because ideas and thoughts were running through my head. I scheduled meetings and social activities almost constantly throughout these two weeks and shared my experiences as my new self. As I started to sleep less and skip nights of sleep, others later told me I seemed agitated and down.

Maybe it is possible to catch these early warning signs and take counter measures before they worsen into mania or depression. This is why I have started to track my behavior starting with mood and sleep. If I can get a baseline of my behavior and know what is ‘normal’ for me, it will be easier to notice when I am outside my normal range. I can alert myself or be alerted by others around me who are monitoring me. Long-term records of mood will also help me experiment to see which things influence my mood. This may give me more control over my mood.

Mood tracking might be a good idea for anyone to do, but it may be especially helpful for people with a bipolar diagnosis. Everyone has mood variation. For bipolars, however, mood swings can be more extreme (in both directions, up and down) , have far worse consequences (psychosis on one end and suicide on the other), change more rapidly, and be more vulnerable to environmental triggers like stress. The good news is that the first changes in mood can happen hours or days before more extreme changes. This gives people a chance to take countermeasures to prevent more extreme states.

The project name refers to the fact that Van Gogh had bipolar disorder.