Seth's Blog

In this 10-minute talk I discuss what I think are the two main principles of experimental design:

1. Something is better than nothing. You learn more from doing something than from thinking about what to do.
2. When you do something, do the smallest easiest thing that will help, that will tell you something you don’t know.

Grad students often fail to understand Principle 1: They worry too much about what to do. Early in grad school, that was my big mistake. Professors often fail to understand Principle 2: They do something more complex than necessary. Failure is much more likely than they realize. My previous post was about such a failure (using genes to predict disease). When I was an assistant professor, I often made this mistake.

From an article by Nicholas Wade in the NY Times:

Since the human genome was decoded in 2003, researchers have been developing a powerful method for comparing the genomes of patients and healthy people, with the hope of pinpointing the DNA changes responsible for common diseases.

This method, called a genomewide association study, . . . has been disappointing in that the kind of genetic variation it detects has turned out to explain surprisingly little of the genetic links to most diseases.

Wade means the genetic variation is surprisingly poor at distinguishing healthy people and sick people. That is the empirical result.

Unlike the rare diseases caused by a change affecting only one gene, common diseases like cancer and diabetes are caused by a set of several genetic variations in each person.

This is the faith-based statement. Wade knows this how? What about the possibility that cancer and diabetes are caused by environmental differences? That there are consistent environmental differences (e.g., dietary differences) between those who get cancer and those who don’t?

I know of no evidence that common diseases like cancer and diabetes are caused by several genetic variations in each person. I know of a lot of evidence that they are caused by the wrong environment — lung cancer caused by smoking, for example.

Preachers say: If you do X, you will go to heaven. In other words, do something that helps me (the preacher) now and you will benefit later. It has been an effective argument. This is what the geneticists have been doing. They say to granting agencies — who believe what they read in the NY Times — if you give us money now we will find the genetic basis of Disease X. Just as there was no clear reason to believe the preachers’ claims, there was no clear reason to believe the geneticists’ predictions. Which unfortunately for them can be shown to be wrong.

The success of my self-experimentation at solving common problems led me to think the environment is more powerful than NY Times readers, or at least NY Times reporters, had been led to believe. Good news for people with problems but bad news for scientists who want large grants. My research was essentially free.

If you have two hammers, how many nails do you see?

I’m in Boston. I had planned to give up fermented foods during this trip and see what happened. Too hard, it turned out. Sitting in a diner, I wondered: where can I get kombucha? The diner sold a bunch of bottled drinks: juice and soft drinks. Foods that taste exactly the same each time, which I call ditto foods and which I believe caused the obesity epidemic. (Because their taste — actually, their smell — is so uniform, a very strong smell-calorie association can build up, making them very tasty and very fattening. Ditto foods are the laser beams of food.) I realized these drinks were exactly the opposite of what I wanted. Fermented foods, because they involve growing bacteria, are inherently more variable than other foods. It is hard to keep constant from batch to batch everything that affects bacterial growth.

Funny thing: the growth in childhood asthma and allergies, now called an epidemic, started at roughly the same time as the obesity epidemic — around 1980. Around 1980, people started to eat a lot more fast food, snack food, and microwaved food (from packages). All ditto foods. All bacteria-free. In home cooking, I think fewer precautions are taken to wipe out all bacteria. You eat what you’ve made soon after cooking, whereas factory food might be eaten weeks or months after production. So factory food has preservatives — and I think the result is overkill, just like antibiotics.

Looking at the food I could buy in Boston was like looking at a post-apocalyptic landscape. Dead food everywhere. Supermarkets, diners, fancy restaurants. Dead food is uniform food; food manufacturers had bludgeoned their products into uniformity. At a Cordon Bleu cooking school, judging from promotional literature, not a word is said about fermented food. In advanced-thinking Cambridge, which you might think would support fermented foods, I found only two stores that sold kefir and only three that sold kombucha. Many people complain about what they call “processed food” but the actual problem is food not processed enough (by bacteria). A better complaint would be about dead food.

I suspect fermented foods are avoided by commercial food makers not only because they are more variable than other food and contain scary bacteria, but also because they are more expensive to make: They require more space and time. The stuff must sit somewhere, taking up space, for days or even weeks, while it ferments. At home, it’s easy: You make it and put it somewhere, and go away and do something else. In a factory devoted to making food, there is nothing else to do and no free space. The monoculture problem.

Karky lost 100 pounds. Here are before and after pics. I like how one person put it: “A to the M to the A to the ZING!”

To protect against C. difficile infection:

What is so frightening about C. difficile is that it is often spurred by antibiotics. The drugs wipe out the targeted illness, like a urinary tract or upper respiratory infection, but they also kill off large portions of the healthy bacteria that normally live in the digestive tract. If a person [who has just taken antibiotics] comes into contact with C. difficile, or already has it, the disruption to the beneficial bacteria creates an opportunity for the harmful bacteria to flourish.

The NY Times article doesn’t mention fermented foods.

Thanks to Ashish Mukharji.