Category: ignorance

False Confidence About What Caused the Newtown Massacre

Seth Roberts3 Comments

New York magazine commenters are usually smart and well-informed. Which is why this comment, on an article about “the forgotten victim”, Nancy Lanza, the shooter’s mother, stands out:

They say money cannot buy happiness [Adam’s father is apparently rich], but when dealing with someone with a mental illness, it can go a long way toward paying to fix unhappiness — it can pay for good doctors, proper medication [emphasis added], care-givers/guardians, all the tools required to secure a property and keep the “patient” safe, AND giving the mentally ill person his ideal living situation, limiting the snits and tantrums that can lead to real anger, which, in turn can lead to acting out.

No doubt this particular commenter is smart and well-informed. Which makes the fact that he or she is perfectly sure that “proper medication” exists so scary, at least if this person had any control over me or anyone who mattered to me. It reminds me of people who think that if you’re fat all you have to do is eat less.

Who is the Richest Person in China?

Seth Roberts6 Comments

If you open the American edition of Forbes, you will find articles about the richest people in America. If you open the Russian edition, you will find articles about the richest people in Russia. If you open the Chinese edition, you will find articles about the richest people in America.

A Russian friend of mine noticed this. He happened to know an sophomore economics major at Tsinghua. It is incredibly difficult to get into Tsinghua and the economics major is the most desirable major of all. To be an economics major at Tsinghua you need a test score that is in something like the top 1 out of 100,000. Staggeringly high. My Russian friend asked the Tsinghua economics major, “Who is the richest person in China?”

The economics major didn’t know. He seemed a little angry. “Why should I know? We’ve never been taught that,” he said.

 

Bacteria are Neither Good nor Bad

Seth Roberts15 Comments

Health experts call bacteria “good” and “bad”. Bad bacteria make us sick. Good bacteria help us digest food, and a few other things. Let me propose another view. Any bacteria (i.e., bacterial species) will make us sick if it becomes too numerous — so all bacteria are “bad”. All bacteria protect us against other bacteria — so all bacteria are “good”. The terms “good” and “bad” are misleading. It is like saying a person is inherently rich or poor. Anyone, given a lot of money, becomes rich. Anyone whose money is taken away becomes poor. Low bacterial diversity or reduction of diversity makes it more likely that one bacterial species can overwhelm its competitors, producing sickness. When this happens, to say that the species (e.g., H. pylori) that became numerous “caused” the sickness (e.g., ulcers) is to seriously misunderstand what happened and how to prevent it from happening. We are taught that our immune system protects us from infection. We should be taught that bacterial diversity does the same thing.

The following story, from a reader of this blog, suggested these ideas:

My wife had a lot of problems, visceral fat that wouldn’t go away being one of the most obvious symptoms. Every time I convinced her to try a ketogenic (= very low carb) diet, she would get sick. I went to NYC to see Paul Jaminet speak. He suggested that she likely had some type of gut infection or dysbiosis. Not a bad theory, as she’d undergone prophylactic antibiotic treatment to clear up an H. pylori infection. (Yes, I know, but at the time it seemed like the thing to do.)

She started putting on weight after that, which is typical.

Finally she gave VLC [very low carb] one last try. She wound up getting inflamed lymph nodes in her thighs. Our doctor was wondering if she might have bovine tuberculosis or the bubonic plague, either of which would explain her symptoms. (The nodes were inflamed, black-and-blue, and sensitive. This is a typical symptom of bovine tuberculosis, and the disease spreads from the gut to the body through the bowel. As we consume raw milk, this wasn’t a crazy theory, but there have been no recorded outbreaks in Connecticut for years and years.) All the tests he did for an infection came back negative, but her symptoms clearly suggested she had one.

Finally she went to see a new OB-GYN. His nurse/dietician reaffirmed everything I’d been telling her, and she finally decided to go fully ketogenic. Once again, she got sick, but this time she decided to tough it out. Sure enough, after many weeks she started feeling better, and more importantly, the weight started coming off, and the visceral fat started reducing.

She did a stool test, and (I haven’t seen the results yet) we were told that she had the obesigenic gut biota. So she started an intensive probiotic regimen. This helped her one negative from the ketogenic diet: constipation.

She’s thrilled with the progress she’s seeing, and her few lingering issues after going primal 2.5 years ago seem to be resolving. The constant yeast infections have abated, and she’s planning a new wardrobe, heaven help me.

There are several interesting things here: 1. A very-low-carb diet made her sick. 2. This happened after antibiotic treatment. 3. Tests for infection were negative. 4. If she waited long enough, the low-carb-induced illness abated. 5. Probiotics helped. 6. Fermented foods didn’t help. At the time of Paul Jaminet’s diagnosis, says the reader, they were already eating plenty of fermented food: “Sauerkraut, yogurt, home-made kefir, the whole drill. No effect.”

How can these observations be explained?

With some general ideas. Each bacterial species keeps similar species in check by competing for the same resources (food and location). No two species need exactly the same things but there is plenty of overlap. For example, Species 1 needs Resources A and B, Species 2 needs Resources A and C. They keep each other in check by reducing the supply of A. Suppose C = carbohydrate. By reducing C, a very-low-carb diet reduces the number of Species 2, making more A available. This allows Species 1 to greatly expand. Maybe this expansion kills off Species 2. Armed with vast amounts of A, Species 1 out-competes other competitors. Its numbers greatly increase, causing sickness.

The notion that some bacteria are good and others are bad is absurd because all are safe in small amounts and all will cause sickness in large amounts. If any one person was replicated in millions or billions of copies it would cause enormous damage, waste and disruption, no matter who it was. Suppose I was genetically replicated so that there were hundreds of millions of me. I only like a few singers, such as Michelle Shocked and Cat Power. There would be a huge undersupply of records by those singers and a huge oversupply of other music. The music industry would collapse. I am a certain size. There would be a huge shortage of clothes of my size and a huge oversupply of clothing of other sizes.

The bacterial ecosystem is not self-correcting. It is the opposite: disruptions tend to spread. Suppose you eat too little carbohydrate. This reduces Species 2 (which needs A and C = carbohydrate). This means there is more Resource A for Species 1 (which needs Resources A and B). Species 1 increases. By virtue of increased numbers, it pushes down its competitors for Resource B. These weakened competitors, which also need D, E, and F, begin to lose battles for those resources against other bacteria that need D, E, and F. They decline in number. No longer with substantial competition for what it needs (A and B), Species 1 multiplies unchecked and causes damage until A and B run out. (Which may be why the reader’s wife, after a long illness, got better.) Fever fights infection because bacteria that grow best at one temperature (normal body temperature) do less well against competitors at a higher temperature.

The tests for infection failed to come up positive because they looked for too few bacteria. According to this view, there are thousands of bacteria inside us that can run out of control. You can test for only a tiny fraction of them. Fermented foods failed to help because they did not provide enough diversity.

We have a huge preference for diversity in what we eat. We much prefer a meal with three foods than one food, for example. The usual view is that this preference evolved because we need many nutrients (e.g., many vitamins) to be healthy. Now I wonder. Maybe the protective effect of bacterial diversity was the main reason. If so, taking a multi-vitamin pill is not going do much good, which is what research suggests.

These ideas are obviously supported by evidence that fermented foods improve health and antibiotics harm health, which I’ve covered many times. They are also supported by two recent studies with a different emphasis. One of them found that teenagers who had more biodiversity near home had more bacterial diversity on their skin. (Maybe there are other important drivers of diversity besides fermented foods.) The other found that people with sinusitis had less bacterial diversity in their nose than people without sinusitis and that increasing diversity tended to prevent sinusitis. Someday the 2005 Nobel Prize for “showing” that ulcers are “caused” by H. pylori will seem as medieval as the 1949 Nobel Prize for prefrontal lobotomies.

The practical consequences of this view include: 1. Antibiotics should be a very last resort. When given, they should be followed by treatments that restore bacterial diversity. The reader’s story suggests restoration of diversity may not be easy. Plainly diversity should be tracked after antibiotics. 2. Epidemiological studies should not just ask how did the germs spread? They should also ask why were they allowed to do harm? Why didn’t natural defenses – the immune system and other bacteria – suppress them to harmless levels? To the epidemiological neglect of immune function we can add neglect of this line of defense. 3. There should be convenient ways to measure one’s bacterial diversity so each of us can learn where we are and what makes it go up and down. 4. Researchers should study what makes bacterial diversity go up and down. Here is a recent study about this: old people living in an old-age home, who ate a restricted diet, had less bacterial diversity than people the same age who lived independently and ate more varied foods.. 5. Researchers should learn the correlates of high and low diversity. Take a group of people, measure their bacterial diversity, track their health for six months.

 

 

 

The Dark Side of Open Source

Seth Roberts15 Comments

A friend writes:

David [her boyfriend, not his name] learned some of the new languages (Android being one ). He says that any programming involving Open Source software requires wading through undocumented code, sloppily written by guys who de facto require one to email them, asking for technical support.

And without the cooperation of these people, one has no chance in hell of figuring out what the next command syntax should be. And a lot of the guys who wrote the code are reluctant to cooperate, because their knowledge of how their own code is supposed to be written and how to run it is their only job security.

Coding for very simple operations, such as connecting an external camera to an Android cell phone, has been proving impossible. He’s been working on it for 10 days now.

David has tried several flavors of Linux kernels and also several brands of smartphone drivers. But it always comes to the same thing. The software won’t run, and there are maybe one or two wrong characters in 20,000 lines of code that made it break, and you don’t know where to start looking. Because the error message doesn’t tell you anything other than it won’t run.

To be fair, I use R (which is open source) many times every day. It has far fewer bugs than the S-plus software it replaced. That it’s free is a huge plus.

The Personal Scientist Who Knew Too Much

Seth Roberts3 Comments

The San Jose Mercury News recently ran a story by Lisa Krieger about a father (Hugh Rienhoff) who found a single-amino-acid mutation that he believes causes his daughter’s growth difficulties.

Born with small, weak muscles, long feet and curled fingers, Beatrice confounded all the experts.

No one else in her family had such a syndrome. In fact, apparently no one else in the world did either.

Rienhoff — a biotech consultant trained in math, medicine and genetics at Harvard, Johns Hopkins and the Fred Hutchinson Cancer Research Center in Seattle — launched a search.

He combed the publicly available medical literature, researching diseases, while jotting down each new clue or theory. Because her ailment is so rare, he knew no big labs or advocacy groups would be interested.

He did some of his own lab work in his San Carlos home, borrowing tools or buying them used online.

A few commercial labs, like the San Diego-based biotech Illumina, offered him help for free. And a wide array of pediatricians, geneticists and neurologists volunteered their opinions.

Over time, he zeroed in on a stretch of genes that control a growth hormone responsible for muscle cell size and number. And he knew he could further target his search — saving time and money by not sequencing Bea’s entire genome, but only the exomes, which are the genes that code for proteins.

This is not a simple upbeat story. The father is a genetic researcher and doctor. I agree, he has made considerable progress in understanding the cause of his daughter’s problem. Not addressed are two questions: 1. Why is he sure he has the right mutation? Perhaps his daughter has other mutations. I’m sure the father understands this, the journalist may not. 2. What about environmental causes? As Aaron Blaisdell’s story shows — Aaron has/had a single-gene genetic disease that vanished when he changed his diet — single-gene diseases may respond to environmental changes. Early work with bacteria emphasized this. If Rienhoff had spent equal effort in trying to find environmental changes that help, he might be further along in discovering them. An obvious place to start would be testing different diets. There is no sign he has done that. His knowledge of genetics, plus the brainwashing that doctors undergo (they are told genes are incredibly important), may have led him to waste a lot of time. Someone with less understanding of genetics may realize better than Rienhoff that knowing what genes have changed may be very little help in finding helpful environmental changes.

Thanks to Allan Jackson.

 

Big Diet and Exercise Study Fails to Find Benefit

Seth Roberts34 Comments

Persons with Type 2 diabetes have an increased risk of heart disease and stroke. They are usually overweight. A study of about 5000 persons with Type 2 diabetes who were overweight or worse asked if eating less and exercise — causing weight loss — would reduce the risk. of heart disease and stroke. The difficult treatment caused a small amount of weight loss (5%), which was enough to reduce risk factors. The study ended earlier than planned because eating less and exercise didn’t help: “11 years after the study began, researchers concluded it was futile to continue — the two groups had nearly identical rates of heart attacks, strokes and cardiovascular deaths.”

Heart disease and stroke are major causes of death and disability. Failure of such an expensive study ($20 million?) to produce a clearly helpful result is an indication that mainstream health researchers don’t understand what causes heart disease and stroke. Another indication is that the treatment being studied (eating less and exercise) was popular in the 1950s. Mainstream thinking about weight control is stuck in the 1950s. It is entirely possible that greater weight loss — which mainstream thinking is unable to achieve — would have reduced heart disease and stroke. If you understand what causes heart disease and stroke, your understanding may lead you to lines of reasoning less obvious than people with diabetes are overweight –> weight loss treatments).

One of the study organizers – Rena Wing, a Brown University professor who studies weight control — told a journalist “you do a study because you don’t know the answer.” She failed to add, I’m sure, that wise people do not give a super-expensive car to someone who can’t drive. You should learn to drive with a cheap car. Allowing ignorant researchers to do a super-expensive study was a mistake. To learn something, do the cheapest easiest study that will help. (As I have said many times.) You should not simply do “a study”. This principle was the most helpful thing I learned during my first ten years as a scientist. In this particular case, I doubt that a $20 million study was the cheapest easiest way to learn how to reduce heart disease and stroke.

I made progress on weight control, sleep, and other things partly because studying myself allowed me to learn quickly and cheaply. If researchers understood what causes major health problems, they would be able to invent treatments with big benefits. That the Nobel Prize in Physiology or Medicine is given year after year to work that makes no progress on major health problems is another sign of the lack of understanding reflected in the failure of this study. I have never seen this lack of understanding — which has great everyday consequences — pointed out by any science blogger or science columnist or science journalist, many of whom describe themselves as “skeptical” and complain about “bad science.”

 

 

The 2012 Nobel Prize in Physiology or Medicine

Seth Roberts4 Comments

As usual, there is plenty of disease and disability in the world: depression, diabetes, heart disease, cancer, stroke, obesity, autoimmune disease, and so on. As usual, the Nobel Prize in Physiology or Medicine — supposed to be given for the most useful research — is given for research with no proven benefit to anyone (except career-wise). Once again implying that the world’s best biomedical researchers — judging by who wins Nobel Prizes — either don’t want to or don’t know how to do useful research.

Once again the press release tries to hide this. “From surprising discovery to medical use” reads one heading. If you read the text, however, you learn there is no actual “medical use”. Here’s what it says:

These discoveries have also provided new tools for scientists around the world and led to remarkable progress in many areas of medicine. iPS cells can also be prepared from human cells. For instance, skin cells can be obtained from patients with various diseases, reprogrammed, and examined in the laboratory to determine how they differ from cells of healthy individuals. Such cells constitute invaluable tools for understanding disease mechanisms and so provide new opportunities to develop medical therapies.

Apparently you can make “remarkable progress” in medicine without helping a single person, which says a lot about what passes for medical progress. Although iPS cells are supposedly “invaluable tools” for understanding disease mechanisms, we are not told a single disease that has thereby been understood or a single therapy that has been developed.

The Guardian printed a roundup of responses to the award. I read it eagerly. Maybe one of the comments will explain how the prize-winning work actually helped someone (besides career-wise). After all, Yamanaka, one of the winners, had previously won the Finland Prize, given to research that “significantly improves the quality of human life today and for future generations”. Paul Nurse says the prize-winning work did such-and-such, “paving the way for important developments in the diagnosis and treatment of disease” unfortunately not saying what those “important developments” are. Martin Evans says:

The practical outcome is that now we not only know that it might be theoretically possible to convert one cell type into another but it is also practically possible. These are very important foundation studies for future cellular therapies in medicine.

Emphasis added. Another comment: “These breakthroughs will ultimately lead to new and better treatments for conditions like Parkinson’s and improve the lives of millions of people around the world.” A bold prediction, given that they have not yet improved the life of even one person. Julian Savescu, an ethicist at Oxford, says “This is as significant as the discovery of antibiotics. Given the millions, or more lives, which could be saved, this is a truly momentous award.”

Year after year, the Nobel Prize in Physiology or Medicine is given for research that, we are told by biologists with huge conflicts of interest, will — no doubt! — be incredibly valuable in the future. Indicating there was no research that might be honored that had already been useful. It is as if you have a baseball award for best hitter but all hitters all over the world strike out all the time so you end up giving the award to people who strike out best. They are the best hitters, you tell credulous sportswriters. They receive the prestigious award for best hitter at an elaborate ceremony, with toasts all around. Nobody says they cannot hit.

 

More Examples of Mainstream Health Care Ignoring the Immune System

Seth Roberts19 Comments

In a recent post I made an obvious point. If our immune systems were stronger, we would need antibiotics less often and antibiotic resistance would become less of a problem. I hadn’t heard this point made (for example, this WHO report fails to say it). This was one example, I said, of how mainstream health care ignores the immune system. Perfectly obvious things, such as this idea about antibiotic resistance, fail to be noticed. I gave five more examples. Since then I have come across even more examples:

1. Hospitals do little to help patients sleep and often interrupt sleep, Nancy Lebovitz pointed out (better sleep –> better immune function). This article describes the problem. One way to improve hospital sleep — beyond don’t wake patients up — would be to provide exposure to strong sunlight-like light in the morning and prevent exposure to sunlight-like light after dark. I found that an hour of sunlight or similar light from fluorescent lamps in the morning improved my sleep. Most fluorescent light resembles sunlight (both have strong bluish components), incandescent light (reddish) does not. Until they install dual lighting systems (bluish light during the day, reddish light at night), hospitals can provide blue-blocker glasses to wear after dark.

2. The book Immortal Bird (sent me by the publisher) tells how Damon Weber, born with a defective heart, had a heart transplant when he was a teenager. After the transplant, problems arose. The doctors involved (at NewYork-Presbyterian ­Hospital/Columbia University Medical Center) took the problems to be signs of transplant rejection. In fact they were due to infection. Drugs given to deal with the mistakenly-assumed rejection suppressed Damon’s immune system. They reduced his ability to fight off the infection and he died. The author of the book, Damon’s father, sued the doctors and hospital for malpractice. The doctors did not exactly “ignore” the immune system, but they apparently failed to fully grasp the danger of immune suppression, even though the infection that killed Damon is common in transplant cases. (Although Columbia Presbyterian charged half a million dollars for the transplant, “three years into the lawsuit the [hospital’s] medical director claimed Damon’s post-op records couldn’t be located.”)

3. I asked a UCSF medical student what she’d been taught about the immune system. “We cover it!” she said. In a section called “Infectious Disease, Immunology, and Inflammation”. What makes the immune system work better or worse? I asked. “If you’re stressed out, it doesn’t work well,” she said. If you’re malnourished, like in Bangladesh. You need “nutrients and vitamins”. (A booklet I got telling me to take less antibiotics told me to “eat healthy”.) She also said the students get entire lectures on how to treat diseases so rare they might never be encountered. There is a whole section on genetics. Sure, they cover it. So superficially that they don’t remember the most basic idea: Better sleep –> better immune function. I said our health care system is built around first, let them get sick. That’s right, she said. Ignoring the immune system is an excellent way to allow people to get sick.

4. Melissa McEwen pointed out that proton pump inhibitors, such as Nexium, reduce the body’s ability to fight infection. They are prescribed for acid reflux and reduce how much acid the stomach makes. Because stomach acid kills bacteria, there should have been far more concern about their safety. “Proton pump inhibitors (PPIs) are among the most widely prescribed medications worldwide [billions of prescriptions]. . . . The collective body of information overwhelmingly suggests an increased risk of infectious complications,” says this article. Because the drugs are so common, the damage is great and, because of more infection, not restricted to those who take them. It could have been avoided by research into treatments that do not harm the immune system.

Assorted Links

Seth Roberts4 Comments
  • Edward Jay Epstein on The Lessons of Le Carre (the spy novelist)
  • Gary Taubes recommends five excellent books, including Weston Price.
  • This article about the Marc Hauser case tells a brief story about a Harvard coverup in the 1960s. “In the late 1960s I was eating lunch in William James Hall with a few fellow assistant professors in the Harvard psychology department when a woman named Patricia Woolf sat down at our table. . . . She asked whether we had heard anything about the fabrication of data by one of our colleagues.”
  • This sad and fascinating post tells how pediatricians encourage Vitamin D deficiency by warning parents to keep children out of the sun. Then, making things even worse, children with broken bones due to Vitamin D deficiency are assumed by pediatricians to be victims of child abuse. “Dr. Carole Jenny, head of the American Academy of Pediatrics Section on Child Abuse, implies such tragic miscarriages of justice simply don’t happen. She then claims, “We have been checking every child with multiple fractures for metabolic bone diseases for several years and have not identified a single child with vitamin D deficiency.” How can that statement be true if every other researcher is reporting infantile and early childhood vitamin D deficiency to be rampant in normal children? Furthermore, how can an infant beaten severely enough to cause multiple fractures not be bruised or in distress? Dr. Jenny cleverly avoids the question.”

Steve Jobs’ Graduation Speech: My Opinion

Seth Roberts26 Comments

In a recent post I said that Steve Jobs seemed to live in a very limited intellectual world. I gave his Stanford graduation speech as an example. Someone asked me to explain. Here is my explanation.

The speech shows no sign of having read a book. It shows no sign of any intellectual interest outside his job.

It makes the insanely self-centered point that “if I had never dropped out, I would have never dropped in on this calligraphy class, and personal computers might not have the wonderful typography that they do.”

It shows no sign of learning from anyone else (except his calligraphy teacher, which hardly counts). It shows no sign of even having noticed anyone else — it is all Steve all the time. It mentions Stewart Brand, but only to comment about the Whole Earth Catalog.

It makes the banal point what seemed like bad news was actually good news (“it turned out that getting fired from Apple was the best thing that could have ever happened to me”).

It ends with a long string of banalities about death: “And yet death is the destination we all share. No one has ever escaped it. And that is as it should be, because Death is very likely the single best invention of Life. It is Life’s change agent. It clears out the old to make way for the new.” A high school student could have said that — at a funeral, perhaps.

This is from someone at the center of an enormous on-going revolution. I tried to find praise for it but all I found was that someone in the Ukrainian government had plagiarized it.