The Hygiene Hypothesis, Pro and Con

According to BBC News, recent research supports the hygiene hypothesis:

Normal bacteria living on the skin trigger a pathway that helps prevent inflammation when we get hurt, the US team discovered. The bugs dampen down overactive immune responses that can cause cuts and grazes to swell, they say.

And other recent research says it’s wrong:

The decades-old “hygiene hypothesis” holds that early exposure to microbes somehow challenges the immune system and strengthens it against allergies. Studies have shown children exposed to bugs by older siblings or attending nursery cut their future allergy risk.

But new work published by the American Thoracic Society casts doubt on this.

The study by Dutch investigators at the Erasmus University found although children in day care got more colds and other infections, they were just as likely as other children to go on to develop asthma or another allergy by the age of eight. The children who went to nursery and who had older siblings had more than quadruple the risk of frequent chest infections and double the risk of wheezing in early life, with no obvious pay off in terms of later protection from allergy.

The original hygiene hypothesis said that exposure to harmful germs (e.g., that cause colds) cuts down on allergy risk. But it’s now clear it’s the exposure to harmless germs (e.g., in dirt) that’s helpful.

Allergies in the UK have tripled in the last 10 years. I believe this is due to greater consumption of food that is germ-free, such as factory food and restaurant food. Shelf-life considerations and food-safety laws, in other words.

Advice given by Allergy UK:

The best advice we can currently give to parents is not to smoke around their children and make sure they have a balanced diet and get plenty of exercise.

Not even close to what I think. My advice is: Feed your kids plenty of fermented food, such as yogurt. I’d bet a lot of money that my advice is better.
Thanks to Mark Griffith.

A Clue About How To Sleep Better

A few nights ago I slept surprisingly well: I woke up feeling more rested than usual. Each morning I judge how rested I feel on a scale from 0 to 100 where 0 = as if I hadn’t slept and 100 = completely drained of tiredness. I got scores of 100 after standing 9 or 10 hours during the day. That showed what was possible but that much standing was unsustainable. Without extreme standing, 99 has seemed to be the maximum.

A few nights ago, I did better. The ratings for that night and the preceding four nights were: 98.9, 98.8, 99, 98.8, 99.2. Doesn’t look like much, but actually the improvement was so clearly unusual I didn’t need records to notice it. If I gave the scores for the preceding 100 nights you’d see it was rare to score above 99. Moreover, I was keeping the amount of animal fat I ate constant, unlike previous nights with scores above 99. The difference between 98.8 and 99.2 is easy to notice. Think of the difference between 12 and 8.

What had improved my sleep? I could think of four unusual things about the preceding day:

1. Several cloves of garlic in the pork-belly soup I ate for lunch. I’d never before added any garlic.

2. I began using f.lux, which reduced the color temperature of my computer screen after sunsight.

3. I’d played Dance Dance Revolution (on the Wii) for 10 minutes at 8 pm. Usually I do it in the morning (much longer, 30-50 minutes).

4. More bike riding than usual (including two long stretches that added up to 66 minutes).

All four seemed unlikely. 1. Who’d heard of garlic improving sleep? Not me. 2. Laptop screens are quite dim compared to sunlight. 3. The amount of exercise was small. I’d played Wii Tennis for longer periods in the evening without noticing any change. DDR in the morning hadn’t made an obvious difference. 4. I’d ridden my bike for 50-odd minutes at a stretch without noticing better sleep. This was only slightly more.

Now I am testing these possibilities. If you have any idea which it is — perhaps it is none of them — please comment.

Kombucha Reduces Free Radicals

Trichloroethylene (TCE) is a common industrial solvent for many years used as an anesthetic. It appears to cause liver damage. A recent experiment with rats asked if kombucha could protect against TCE damage. For at least two measures, it did. TCE raised free radicals in the blood by a factor of 6; kombucha reduced the increase to a factor of 2. TCE also increased gamma-glutamyl transferase (GGT) activity, a mark of liver damage; kombucha reduced GGT activity to normal levels.

The paper’s bibliography includes a reference to a survey of kombucha’s health effects:

Dufresne C, Farnworth E: Tea, kombucha health: a review. Food Res Int 2000, 336:409-421.

The researcher brewed the kombucha that was used (for about ten days). Weirdly the source of the kombucha is given under “Competing Interests” at the end of the paper.
This article will appear in the journal Chinese Medicine — but I have not found kombucha for sale in Beijing.

Congratulations, Andrew Rivkin

Andrew Rivkin writes about climate change for the New York Times. One of the stolen emails says:

At 17:07 27/10/2009, Michael Mann wrote:

Hi Phil,

p.s. be a bit careful about what information you send to Andy and what emails you copy him in on. He’s not as predictable as we’d like

In other words: Most reporters are predictable. Meaning they repeat what they are told instead of thinking for themselves. Otherwise there would be no need to say this.

Think about it. Michael Mann, a respected climate scientist, thinks that whatever line he and Phil Jones, another respected climate scientist, are pushing is so poorly supported by the evidence that they worry about a New York Times reporter finding holes in it! Independent thinking, even by someone without technical training, worries them! Really, it’s hard to avoid concluding that these guys are clowns, propped up by all sorts of people (journalists, Al Gore, many others) who benefit from a false certainty about this stuff.

Please, someone tell me: Why should I believe climate models? Have their predictions (not their fits) been compared to what actually happened?

Senator Grassley Asks Med Schools Their Policies On Ghostwriting

Medical ghostwriting is plagiarism with a bullet: not only do med-school profs get the benefits of a published article they didn’t write, that published article — written by a drug-company hack — is inevitably misleading, causing doctors to prescribe a drug that is worse than they think. (Which is the whole point.) Patients who take the drug are the big losers.

This sort of thing is so patently awful — especially the harm done to millions of sick innocent people — that you’d think everyone finds it repulsive. Quite the opposite. Living breathing med school professors, such as New York University professor Lila Nachtigall, have trouble seeing what’s so bad about it. The practice appears so common that Senator Grassley asked the ten top medical schools, such as Harvard, Johns Hopkins, and UCSF, to say their policies about it. He’s asking them: Do you consider plagiarism wrong? Except it’s much worse than plagiarism. Although several say on their websites that it’s wrong, Duke University says that “Severe and/or repeated offenses will result in formal disciplinary action”– in other words, non-severe examples are okay! At least the first time. “Formal disciplinary action” can be as mild as a letter. At Duke, at least, they have trouble grasping how awful it is.

This might seem to have nothing in common with self-experimentation. Self-experimentation can be done by anyone, costs nothing, and is a way to figure out helpful truths; whereas almost no one can get a drug company to write a paper for them (you need to be at a top medical school), drugs are a hundred-billion-dollar/year business, and this sort of ghost-writing is done to hide helpful truths. In a better world, they really would be worlds apart. But you are reading this not because I did self-experimentation but because I did self-experimentation that found out something useful and surprising — the Shangri-La Diet and new ideas about sleep and mood. A big reason it did so was that the experts in those fields — such as the relevant med school professors — were utterly and completely asleep, so to speak. They were incapable of making significant progress. Extreme careerism — putting one’s career ahead of everything else — is no doubt one reason. They could have done what I did. Fat weight-control profs could have tested different diets on themselves, for example. But doing good research would be harmful to their career (e.g., not enough publications), so they don’t do it. Medical ghostwriting helps their career, so they take advantage of it. So what if millions of sick people are harmed by these decisions.

My surprisingly-productive self-experimentation and the staggeringly careerist decisions of med school profs are two sides of one coin: the profound stagnation in health care. The complete inability of those in charge to innovate effectively. Drug companies are businesses that make drugs. They are not going to explore non-drug low-cost solutions, such as those I explored. Nothing, however, prevents med school profs from doing so — at least, nothing except their extreme careerism. My self-experimentation shows what could have been done. It shows that the health questions we face (e.g., how to lose weight) have solutions much better than a new drug. The widespread practice of medical ghostwriting is one indication why those solutions haven’t been found. Failure to find new solutions means problems have stacked up unsolved, getting worse and worse (the obesity epidemic, the allergy epidemic, etc.). It’s usually called a healthcare crisis — but it’s really a health crisis.

Benefits of Kefir: N=1

A year and a half ago, Charles Richardson was given antibiotics for an ulcer. He writes:

When they put me on the course of antibiotics for the ulcer, my digestion absolutely went south. Stools became runny and smelly and irregularly timed. Even though I took a lot of supposedly high-end probiotic capsules, that went on for months after the antibiotics.

Six months ago — a year after the antibiotics — he started drinking kefir because of this blog. “After about a month [of kefir], I was back to normal,” he writes. He got the starter culture from kefirlady.com (where they cost $20 cash).

More recently he has seen further improvements:

I had a number of food allergies, particularly wheat. If I ate any wheat, I’d get hemorrhoids immediately, and sometimes what looked like a herpes outbreak.

I’ve had that for 30 years or so, but it appears to have gone away in the last month. I had to eat some pasta at a formal dinner, and was expecting a reaction, but had none. I was shocked. I also have a similar reaction to chicken, and had the some non-experience with some of that recently.

I don’t know to what I can attribute that change. The kefir could have helped,and possibly the Vitamin D [about 4000 units/day]. I also started take an amino acid dipeptide of L-glutamine/L-alanine. https://www.kyowa-usa.com/brands/sustamine.html) [about 10 g/day]

This is informative for several reasons.

First, the bad effects of the antibiotics lasted a really long time (a year). This indicates how bacteria-poor a normal American diet is. Richardson probably ate healthier than normal given that he once owned a health-food store.

Second, expensive probiotics didn’t help. This is why I make kombucha and yogurt, to have more quality control. And yogurt is surely closer to what our ancient ancestors ate to get bacteria than probiotic capsules.

Third, the kefir took about a month to solve the problem. This gives an idea of the time it takes to repopulate your intestine with bacteria. And thus how long you should try this or that solution before giving up.

More About What Causes MS

In an earlier post I linked to a poll at This Is MS that asked if there is a correlation between getting red in the face after exercise and having multiple sclerosis. Such a correlation would support Paulo Zamboni’s idea that MS is due to poor blood circulation in the brain.

A poll at This Is MS is likely to be answered by people who have MS. Nancy Lebovitz realized she could help get answers from people who don’t have MS — crucial to learning if there is a correlation — by posting the poll on her LiveJournal page.

The two polls taken together show a strong correlation. Out of 40 people with MS, 72% get red-faced. Out of 27 people without MS, 22% get red-faced. Thanks, Nancy.

A Fourth Thing Elizabeth Kolbert Didn’t Know

Elizabeth Kolbert, the New Yorker staff writer, did not know that Phil Jones, a climate-change scientist, manuevered to keep hidden information that disagreed with his conclusions. Here is what one of the damning emails gathered from the University of East Anglia’s Climate Research Unit said:

From Phil Jones [head of the Climate Research Unit]. To: Michael Mann. Date: May 29, 2008
“Can you delete any emails you may have had with Keith re AR4? Keith will do likewise.”

To keep them from being exposed via a Freedom of Information law. Robin Hanson and Tyler Cowen think this is no big deal. I disagree. Yes, I said before this happened that the consensus was likely to appear stronger than it is and that bloggers were a powerful force toward truth — both of which this episode merely supports rather than reveals. And, yeah, it’s just email; the really damning info is the tree-ring data reanalyzed by Stephen McIntyre.

The reason I think this is important is two-fold. First, this is not a smoking gun. Global warming does not equal the honesty of Phil Jones. But it is a powerful piece of evidence that climate skeptics can use to convince anyone that the consensus isn’t as consensus-y as it appears. Second, it exposes what Kevin Trenberth (a proponent of man-made global warming) really thinks. This is something that few knew until now. Here is what he really thinks:

The fact is that we can’t account for the lack of warming at the moment and it is a travesty that we can’t. The CERES data published in the August BAMS 09 supplement on 2008 shows there should be even more warming: but the data are surely wrong. Our observing system is inadequate.

The data are surely wrong. Trenberth, being human, is going to put the best possible spin on things, the spin most consistent with what he has said many times . . . and this is what he comes up with. Support for the idea of global warming is entirely based on climate models. No one has created a mini-Earth and done experiments. If the data and models don’t agree, there is no reason to believe the models. And if you don’t believe the models you have no reason to believe in global warming. Is Trenberth an ignoramus whose honest assessment of the situation (the models and the data profoundly disagree) should be ignored? Of course not. He doesn’t draw the obvious conclusion (the models are wrong) but nothing prevents the rest of us from doing so.

Just to be clear: I completely agree with Robin’s larger point that this sort of thing supports prediction markets. And I think reduced reliance on fossil fuel would be a very good thing.

Three Things Elizabeth Kolbert Doesn’t Know.