Seth's Blog

Patrick Tucker, an editor at The Futurist, posted a request on the Quantified Self Forums for “astounding” predictions based on self-quantification. He is writing a book about using data to make predictions.

Here are examples from my self-measurement:

1. Drinking sugar water causes weight loss. The self-quantification was measuring my weight. It began when I found a new way to lose weight, which pushed me to try to explain why it worked. The explanation I came up with — a new theory of weight control — made two predictions that via self-experimentation I found to be true. That gave me faith in the theory. Then the theory suggested a really surprising conclusion, that loss of appetite during a trip to Paris was due to the sugar-sweetened soft drinks I had been drinking. If so, drinking sugar water should cause weight loss. (The nearly-universal belief is that sugar causes weight gain, of course.) I tested this prediction and it was true. More.

2. Seeing faces in the morning improves mood the next day (but not the same day). This is so surprising I’ll spell it out: Seeing faces Monday morning improves my mood on Tuesday but not Monday. For years I measured my sleep trying to reduce early awakening. Finally I figured out that not eating breakfast helped. There was no breakfast during the Stone Age; this led me to take seriously the idea that other non-Stone-Age aspects of my life were also hurting my sleep. That was one reason I decided to watch to watch a certain TV show one morning. It had no immediate effect. However, the next morning I woke up feeling great. Via self-measurement of mood, I determined it was the faces on TV that produced the effect, confirmed the effect many times, and learned what details of the situation (e.g., face size) controlled the effect. More.

3. One-legged standing improves sleep. Via self-measurement I determined that how much I stood during a day controlled how well I slept. If I stood a long time, I slept better. Ten years later I woke one day after having slept much better than usual. The previous day had been unusual in many ways. One of them was so tiny that at first I overlooked it: I had stood on one leg a few times. Just for a few minutes. Yet it turned out that it was the one-legged standing that had improved my sleep. Without the previous work on ordinary standing I would have ignored the one-legged standing — it seemed trivial.

4. Butter is healthy. I found that butter improved how fast I can do arithmetic problems. No doubt it improves brain function measured in other ways. Because the optimum nutrition for the brain will be close to the optimum nutrition for the rest of the body — at least, this is what I believe — I predict that butter will turn out to be healthy for my whole body, not just my brain.

5. Mainstream Vitamin D research is all messed up. Via self-measurement I confirmed Tara Grant’s conclusion that taking Vitamin D3 in the morning (rather than later) improved her sleep. It improved my sleep, too. When I had taken it at other times of day I had noticed nothing. Apparently the timing of Vitamin D — the time of day that you take it — matters enormously. Take it at the right time in the morning: obvious good effect. Take it late in the evening: obvious bad effect. Vitamin D researchers haven’t realized this. They have neither controlled when Vitamin D is taken (in experiments) nor measured when it is taken (in surveys). Because timing matters so much it is as if they have done their research failing to control or measure dose. If you fail to control/measure dose, whatever conclusion you reach (good/no effect/bad) depends entirely on what dose your subjects happened to take. And you have no idea what dose that is.

I have blogged many times about biohacker Tara Grant’s discovery that she slept much better if she took Vitamin D3 in the morning rather than later. Many people reported similar experiences, with a few exceptions. Lots of professional research has studied Vitamin D3 but the researchers appear to have no idea of this effect. They don’t control the time of day that subjects take D3 and don’t measure sleep. If the time of day of Vitamin D3 makes a big difference, measuring Vitamin D3 status via blood levels makes no sense. Quite likely other benefits of Vitamin D3 require taking it at the right time of day. Taking Vitamin D3 at a bad time of day could easily produce the same blood level as taking it at a good time of day. (more…)

• The corruption of science by research grants. This reminds me of a BBC documentary called something like Science Under Attack. It was hosted by a Nobel Prize winner (Biology) named Paul Nurse. Part of it was about “climate change denialism”.  If you don’t believe that humans are dangerously warming the planet, Nurse implied, you are somehow attacking science. When people who win Nobel Prizes cannot see that AGW is a crock, something curious has happened.
• Edward Jay Epstein interviews DSK. “”Thank you so much for your interest in this case,” he says.”
• Researcher discovers new treatment for her own vertigo. ” A University of Colorado School of Medicine researcher who suffers from benign paroxysmal positional vertigo (BPPV) and had to “fix it” before she could go to work one day was using a maneuver to treat herself [the usual treatment] that only made her sicker. “So I sat down and thought about it and figured out an alternate way to do it. Then I fixed myself and went in to work” and [thereby] discovered a new treatment for this type of vertigo.”

Thanks to Melissa Francis.

A friend of mine who worked in a biology lab said the grad students and post-docs joked about the clinical-relevance statements included at the end of papers and grant proposals: how the research would help cure cancer, retard aging, and so on. It was nonsense, they knew, but had to be included to help funding agencies justify their spending.

Principal investigators never say such things. Are they wiser than grad students and post-docs? Fortunately for the rest of us, actions speak louder than words. An action — actually, a lack of action — that suggests that P.I.’s know their research has little connection to curing cancer, etc., is 50 years of  widespread indifference by cancer researchers to the possibility that their research uses a mislabeled cell line. For example, you think you are studying breast cancer cells but you are actually studying melanoma cells. A recent WSJ article says that the problem was brought to the attention of cancer researchers in 1966 but they have been “slow” to do anything about it:

University of Washington scientist Stanley Gartler warned about the practice [of using mislabelled cells] in 1966. He had developed a pioneering technique using genetic markers that would distinguish one person’s cells from another. Using the process, he tested 20 of the most widely used cancer cell lines of the era. He found 18 of the lines weren’t unique: They were Ms. Lacks’ cervical cancer. . . . A decade after publication of his findings Gartler attended a conference and introduced himself to a scientist. Dr. Gartler recalled the man told him, “‘I heard your talk on contamination. I didn’t believe what you said then and I don’t believe what you said now.’ “

What he meant was: I ignored what you said. Yet it costs only $200 to check your cell line. Fifty-plus years later, mislabeled cell lines remain a big problem. “Cell repositories in the U.S., U.K., Germany and Japan have estimated that 18% to 36% of cancer cell lines are incorrectly identified,” says the article. This indicates considerable indifference to the possibility of mislabeling.

If you truly wanted to cure breast cancer, would you spend $200 (out of a grant that might be $100,000/year) to make sure you were using a relevant cell line? Of course. If you were trying to cure your daughter’s breast cancer or your mother’s melanoma, would you make absolutely sure you were using the most relevant cell line? Of course. I conclude that a large fraction of cancer researchers care little about the practical value of their research.

I believe that one reason my personal science found new solutions to common problems (obesity, insomnia, etc.) is that my overwhelming goal was to find something of practical value. I wasn’t trying to publish papers, impress my colleagues, renew a grant, win awards, and so on. No doubt many cancer researchers want to cure cancer. But this 50-year-and-not-over chapter in the history of their field suggests that many of them have other more powerful motivations that conflict with curing cancer.

Thanks to Hal Pashler. Hal’s work on “voodoo neuroscience” is another instance where the guilty parties, I believe, knew they might be doing something wrong but didn’t care.

• ALS patients test home-brewed drug themselves
• Vitamin K in American foods. I was surprised there is a lot more Vitamin K in chicken than other meats.
• Value of early exposure to microbes.
• 40+ years of mislabelled cell lines in cancer research. “Nearly 40 years later, Dr. Masters, in a study of scientific papers published between 2000 and 2004, found nearly 1,000 citations of the same contaminated cancer lines revealed in Dr. Gartler’s 1966 findings, which have since been replicated many times using more advanced techniques. “They are either crooks or stupid,” said Dr. Masters.”

Thanks to Peter Spero and Hal Pashler.

Did you know that magnesium can reduce constipation? I didn’t. Did you know that constipation can cause bleeding under your skull (subarachnoid hemorrhages), which are earth-shatteringly painful? Apparently a lot of doctors who treat subarachnoid hemorrhages don’t know this. Here is a story from Metafilter:

A year after [cancer] chemo ended I had . . . 4 aneurysms (subarachnoid bleeds) in 12 days. These aneurysms (subarachnoid hemorrhages) were serious agony, the most pain I’ve ever experienced. . . . It’s like the World Trade Center falling down in one’s head, involuntary non-stop screaming, passing out from the pain kind of thing. . . . None of the docs could figure out what these aneurysms were from. They all seemed totally mystified. They gave me a very risky test, brain surgery basically, a brain endoscopy that meant putting a probe into my brain. I had to sign papers that it wasn’t their fault I came out a vegetable.

Several lumbar punctures. 2 CT scans then an MRI. Then my neurologist wanted me to do a really risky test, that involved stopping my heart momentarily. . . . The chances of surviving just one of these aneurysms isn’t good: “An estimated 10-15% of patients die before reaching the hospital. Moreover, mortality rate reaches as high as 40% within the first week, and about 50% die in the first 6 months.” So I felt forced to take this dangerous test. . . .

[I] looked at when the aneurysms happened and the relief I experienced in the Emergency Ward when I’d been injected with magnesium. I googled magnesium and realized its help in treating constipation. I’d been constipated for over a year from the chemo and pain meds for the chemo pain. I realized I had these aneurysms after trying to go to the toilet, from straining. The neurologist didn’t want to hear about constipation . . . . None of the docs asked me about constipation. . . .

I self medicated with magnesium citrate, which relieves constipation in a different way than laxatives, it brings water into the colon, which helps the evacuation process a lot. Calcium and magnesium citrates combined, to be exact. And that did the trick, instantly. No more aneurysms. No more dangerous tests. No more brain surgeries.

I wonder if blood tests showed she was magnesium deficient. I also suspect fermented foods would have helped. Chemo causes constipation, I’m guessing, because it kills intestinal microbes, which fermented foods replace.

If you are nickyskye (the author of this) I hope you will contact me, I would like to write more about it and I have some questions.

Thanks to Melissa McEwen.

• A “safe starch” lowers HDL.
• DIY clinical trials
• omega-3 content versus mercury content of fish: a handy guide.
• Predictions of climate models versus reality. I have only seen careful prediction-vs-reality comparisons made by AGW skeptics. Those who believe humans are dangerously warming the planet appear to be silent on this subject.
• UNESCO’s list of “intangible cultural heritage”. I like to think the items on the list are clues to human nature.

Thanks to David Cramer and Nadalal.

This is me a few days ago. I did a choice reaction time task many times. Each dot is a session with enough trials to supply 32 correct answers.The y axis is in “percentile” units, meaning speed relative to recent performance. If my speed was at the average of recent performance, the percentile would be 50, for example. Higher percentiles = better performance = faster (shorter reaction time). Each point is a mean; the vertical bars are standard errors. The dotted line is the median of the means.

The graph shows that Friday afternoon I was suddenly unusually slow. After dinner, I returned to normal. A change from 60%ile to 20%ile to 60%ile resembles an IQ change from 105 to 87 to 105 (an 18-point change).

At the same time accuracy was roughly constant:

Because accuracy was roughly constant, the change in speed was not due to a shift on a speed-accuracy tradeoff function.

There are two puzzles here. 1. Why were my scores low Friday afternoon? 2. Why did they recover after dinner? On Friday I didn’t feel well. As a result, I didn’t eat much. Maybe my blood sugar was lower than usual. I usually eat 30 g butter twice/day. On Friday I didn’t have any. At dinner I did have moderate amounts of pork fat (but not butter) and sugar (in lemon citron tea). Friday 6 pm I had a cup of black tea. Although I haven’t noticed effects of tea on these scores, there’s a first time for everything.

Here is a clue to what makes my brain work well (= fast), I conclude. Butter causes sudden improvement, I have found; which makes it plausible that lack of butter (and other animal fat) could cause sudden degradation. Another possibility was that my blood sugar was low Friday afternoon. (I didn’t think of this at the time, and didn’t measure it.)  I’m surprised that something as important as brain function would be as fragile as these results imply. When various nutrient deficiencies are studied with conventional measures, it generally takes weeks or months without the nutrient for the bad effects to become apparent. It takes many weeks without Vitamin C to get scurvy, for example.

These results raise the intriguing possibility that everyone has sudden ups and downs in brain function and that these ups and downs can be detected at high signal/noise ratios. If so, we can use these ups and downs to learn how to make our brains work well. These results also imply — because my choice reaction time test required only a laptop — that anyone can detect them, study them, and learn what causes them. No experts needed. What a change that would be.

In a recent editorial in Nature (gated), the research head of a drug company complained that scientists working for him could not repeat almost all of the “landmark” findings in cancer research that they tried to repeat. They wanted to use these findings as a basis for new drugs.  An article in Reuters summarized it like this:

During a decade as head of global cancer research at Amgen, C. Glenn Begley identified 53 “landmark” publications — papers in top journals, from reputable labs — for his team to reproduce. Begley sought to double-check the findings before trying to build on them for drug development. Result: 47 of the 53 could not be replicated.

Yet these findings were cited, on average, about 200 times. The editorial goes on to make reasonable suggestions for improvement based on differences between the findings that could be repeated and those that could not. The Reuters article goes on to describe other examples of lack of reproducibility and includes a story about why this is happening:

Part way through his project to reproduce promising studies, Begley met for breakfast at a cancer conference with the lead scientist of one of the problematic studies. “We went through the paper line by line, figure by figure,” said Begley. “I explained that we re-did their experiment 50 times and never got their result. He said they’d done it six times and got this result once, but put it in the paper because it made the best story.

Okay, cancer research is less trustworthy than someone just barely outside it (Begley) ever guessed. Apparently careerism is one reason why. What is unexplained in both the Nature editorial and the Reuters summary is how research can ever succeed if things aren’t reproducible. Science has been compared to a game of Twenty Questions. Suppose you play Twenty Questions and 25% of the answers are wrong. It’s hopeless. In experimental research, you generally build on previous experimental results. The editorial points out that the non-reproducible results had been cited 200 times but what about how often they had been reproduced in other labs? The editorial says nothing about this.

I can think of several possibilities: (a) Current lab research is based on experimental findings of thirty years ago when (for unknown reasons) careerism was less of a problem. Standards were higher, there was less pressure to publish, whatever. (b) There is a silent invisible “survival of the reproducible”: Findings that can be reproduced live on because people do lab work based on them. The other findings are cited but are not the basis of new work. (c) There is lots of redundancy — different people approach the same question in different ways. Although each individual answer is not very trustworthy their average is considerably more trustworthy.

Leaving aside the mystery (how can science make any progress if so many results are not reproducible?), the lack of reproducibility interests me because it suggests that the pressure to publish faced by professional scientists has serious (bad) consequences. In contrast, personal scientists are under zero pressure to publish.

Thanks to Bryan Castañeda.

A New York lawyer named Greg reports remarkably clear evidence about the effect of butter on blood lipid levels: It improved them. For a few years he measured his HDL and LDL regularly with a home cholesterol device. For unrelated reasons, he started eating more butter. He ate a half stick (about 60 g)/day, like me. Here’s what happened. (more…)