The Personal Scientist Who Knew Too Much

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.

 

The Reddit Protein Powder Tests

A few months ago, a Redditer with access to a protein measurement device offered to measure the protein content of protein powders that readers sent him. He got about twenty samples, presumably from all over the United States. Most of them turned out to have reasonable amounts of protein but four had much less than expected.

The tester interpreted the results here. One of the tested brands, American Pure Whey, clearly has problems. Call it a positive control. By confirming those problems, the rest of the measurements gain credence. One company whose protein powder scored low is Gaspari. Unfortunately I cannot read their reply, which appears on my browser without text.

I look forward to more truth-in-advertising tests. It is really helpful that the data is public — in this case, via Google Docs. Jimmy Moore (of Livin’ La Vida Low Carb) has measured the effect of several supposedly low-carb-friendly products on his blood sugar. His results are here.

Thanks to Eric Meltzer.

The Growth of Personal Science: Implications For Statistics

I have just submitted a paper to Statistical Science called “The Growth of Personal Science: Implications For Statistics”. The core of the paper is examples, mostly my work (on flaxseed oil, butter, standing, and so on). There is also a section on the broad lessons of the examples — what can be learned from them in addition to the subject-matter conclusions (e.g., butter makes me faster at arithmetic). The paper grew out of a talk I gave at the Joint Statistical Meetings a few years ago, as part of a session organized by Hadley Wickham, a professor of statistics at Rice University.

I call this stuff personal science (science done to help yourself), a new term, rather than self-experimentation, the old term, partly because a large amount of self-experimentation — until recently, almost all of it — is not personal science but professional science (science done as part of a job). Now and then, professional scientists or doctors or dentists have done their job using themselves as a subject. For example, a dentist tests a new type of anesthetic on himself. That’s self-experimentation but not personal science. Moreover, plenty of personal science is not self-experimentation. An example is a mother reading the scientific literature to decide if her son should get a tonsillectomy. It is personal science, not professional self-experimentation, whose importance has been underestimated.

An old term for personal science might be amateur science. In almost all areas of human endeavor, amateur work doesn’t matter. Cars are invented, designed and built entirely by professionals. Household products are invented, designed and built entirely by professionals. The food I eat comes entirely from professionals. And so on. Adam Smith glorified this (“division of labor” — a better name is division of expertise). There are, however, two exceptions: books and science. I read a substantial number of books not by professional writers and my own personal science has had a huge effect on my life. As a culture, we understand the importance of non-professional book writers. We have yet to grasp the importance of personal scientists.

Professional science is a big enterprise. Billions of dollars in research grants, hundreds of billions of dollars of infrastructure and equipment and libraries, perhaps a few hundred thousand people with full-time jobs, working year after year for hundreds of years. Presumably they are working hard, have been working hard, to expand what we know on countless topics, including sleep, weight control, nutrition, the immune system, and so on. Given all this, the fact that one person (me) could make ten or so discoveries that make a difference (in my life) is astonishing — or, at least, hard to explain. How could an amateur (me — my personal science, e.g., about sleep is outside my professional area of expertise) possibly find something that professional scientists, with their vastly greater resources and knowledge and experience, have missed? One discovery — maybe I was lucky. Two discoveries — maybe I was very very very lucky. Three or more discoveries — how can this possibly be?

Professional scientists have several advantages over personal scientists (funding, knowledge, infrastructure, etc.). On the other hand, personal scientists have several advantages over professional scientists. They have more freedom. A personal scientist can seriously study “crazy” ideas. A professional scientist cannot. Personal scientists also have a laser-sharp focus: They care only about self-improvement. Professional scientists no doubt want to make the world a better place, but they have other goals as well: getting a raise, keeping their job, earning and keeping the respect of their colleagues, winning awards, and so on. Personal scientists also have more time: They can study a problem for as long as it takes. Professional scientists, however, must produce a steady stream of papers. To spend ten years on one paper would be to kiss their career goodbye. The broad interest of my personal science is that my success suggests the advantages of personal science may in some cases outweigh the advantages of professional science. Which most people would considered impossible.

If this sounds interesting, I invite you to read my paper and comment. I am especially interested in suggestions for improvement. There is plenty of time to improve the final product — and no doubt plenty of room for improvement.

Assorted Links

Thanks to Bryan Castañeda.

Last Weekend’s Quantified Self Conference

Last Saturday and Sunday there was an international Quantified Self Conference at Stanford. I attended. In Gary Wolf’s introductory talk, he said there are 70 Quantified Self chapters (New York, London, etc.) and 10,000 members. I was especially impressed because I recently counted about 50 chapters. One new chapter is Quantified Self Beijing. It has its first meeting — in the form of a day-long conference — in nine hours and I haven’t quite finished my talk (“Brain Tracking: Why and How”). Please indulge me while I procrastinate by writing about the Stanford conference.

Here are some things that impressed me:

Office hours. A new type of participation this year was “office hour”, meaning you sit at a table for an hour. My office hour, during which two people showed up, was the most pleasant and informative hour of the whole conference for me. I thank Janet Chang for suggesting I do this.

Robin Barooah
used a measure of how much he meditated, which he collected via an app he made, to measure his depression. When he was depressed, he didn’t meditate. Depression is half low mood, half inaction. It is very rare that the inactive side of it is measured. It is so much easier to ask subjects to rate their mood, but this has obvious problems. Robin inadvertently found a way to measure level of activity over long periods of time. He also found that participation in an experiment that tested a PTSD drug caused long-lasting improvement, another idea about depression I’d never heard before. At dinner, Robin told me that his partner, when they’re at a restaurant, has sometimes said “God bless Seth Roberts” for allowing her to eat butter without guilt.

Steve Jonas, from QS Portland, told me that he spent a long time (many weeks) doing some sort of mental test. During one of those weeks, he consumed butter a la Dave Asprey, in coffee. Much later he analyzed the results, computing an average for every week, and noticed that during the week with butter his performance was distinctly better than performance on other weeks. I hope to learn more about this. Steve also gave a talk about learning stuff using spaced repetition. He noticed that learning new stuff increased his curiosity. After he used spaced repetition to learn stuff about Mali, for example, he became more interested in reading news stories about Mali. I think this is an important conclusion about education, the way rote learning and encouragement of curiosity are not opposites but go together, that I have never heard before.

Larry Smarr, a computer science professor at UC San Diego, gave a talk called “Frontiers of Self-Tracking” centered on his Crohn’s disease. I was struck by what was missing from his talk. He began self-tracking before the Crohn’s diagnosis and clearly the self-tracking helped establish the diagnosis. However, you don’t need to self-track to figure out you have Crohn’s disease, roughly everyone who has gotten this diagnosis did not self-track. I couldn’t figure out how much the self-tracking helped. Crohn’s is generally associated with frequent diarrhea, which is exactly the opposite of hard to notice. Larry said nothing about this. Later he talked about massive amounts of personalized genetic data that he was getting. I couldn’t see how this data could possibly help him. Isn’t self-tracking supposed to be helpful? If I had a serious disease, I would want it to be helpful. At the same time, judging from his talk, he seemed to be ignoring the many cases where people have figured out how to better live with their Crohn’s disease. I would have liked to ask Larry about these gaps at his office hour but I had an eye problem that caused me to miss it.

I asked Nick Winter, cofounder of Skritter, what he thought of the recent Ancestral Health Symposium at Harvard (August 2012), which we both attended. He didn’t like it much, he said, but it more than justified itself because Chris Kresser’s talk about iron led him to get his iron checked. It turned out be off-the-charts high. Partly because oysters, partly because of red meat. I think he said he has since donated blood and it came down. I hadn’t previously heard of this danger of eating red meat. Again I discussed with Nick why he found that butter had a bad effect on his cognitive performance, the opposite of what I found. One possibility is that the butter slowed digestion of his lunch, thus reducing glucose in his blood at the time of the cognitive tests. But this does not explain why a certain drug eliminated the effect of butter.

In his talk, Paul Abramson, a quant-friendly San Francisco doctor, said that mainstream medicine is “riddled with undisclosed conflicts of interest”. I hope to learn more about this.

Jon Cousins contributed a neat booklet about what he had learned and not learned from starting Moodscope. What he hadn’t learned was how to make a sustainable business out of it. I suggested to him that he might be able find professors who would apply for grants with him that would use Moodscope as a research tool. The grants would pay Jon a salary and might include money for software development. Mood disorders are a huge health problem — depression is sometimes considered the most costly health problem of all, worldwide — and Moodscope is a new way to do research about them. Paying Jon a salary for a few years would cost much less than assembling a similar-sized sample (Moodscope has thousands of users) from scratch. I wonder how professors who do research on mood disorders will see it.

Assorted Links

Thanks to Tucker Goodrich and Allan Jackson.

Bic For Her and Personal Science

Bic’s new line of pens (Bic for Her) was greeted with scorn by Amazon reviewers. David Vinjamuri, experienced in brand marketing, guessed that the reason for the debacle was that the persons who approved the product were quite different than the persons expected to buy it.

Brand companies are not good at assigning authentic consumers [= consumers of their brands] to work on their brands. They [wrongly] assume that [their] lack of personal experience with the product can be made up [for] by lots of analysis. It is very, very hard to imagine that the people who made the decision to launch “Bic for Her” were the same [people] expected to buy them. And that’s why the huge majority of consumer brand launches fail. There are lots of ways to make an awful mistake, but some of the worst could be avoided if consumer companies were staffed by actual consumers.

Health care has the same problem. In health care, the persons who devise a new treatment (a new treatment for acne, asthma, arthritis, diabetes, whatever) are usually 100% distinct from the persons expected to use that treatment. For example, roughly 0% of acne researchers have acne.

If Vinjamuri is right — and I think he is — this explains a lot about the awfulness of modern health care — the terrible side effects of Accutane, for example. And it explains why personal science works so much better. When personal scientists search for a solution to a health problem (e.g. acne), they are 100% the same as the people who will use the solution. No wonder the solutions they find are so much better than what a doctor would prescribe.

50 Years of Knuckle Cracking Did Not Produce Arthritis

Warned by relatives that knuckle cracking causes arthritis, Donald Unger decided to crack only the knuckles of his left hand. For 50 years he frequently cracked his left hand, never his right. Finally he wrote a letter to a scientific journal (in which he calls himself “the author”) pointing out that he did not have arthritis in either hand, supporting the conclusion of another study which studied a much smaller amount of knuckle cracking.

Thanks to Bryan Castañeda via Now I Know.

Assorted Links

 

Want to Track Your Brain Function?

I am looking for people who want to try a mental test I have developed to track brain function. You do it on your laptop, once or more per day. One test session takes three minutes. For five years, I’ve been using various tests to track my brain function — first, balance, then, for a long time, arithmetic speed. The new test is better than these earlier tests, at least for me, because I find it enjoyable, which makes it easy to do several times/day. Via brain tracking, I have found that flaxseed oil and butter make my brain work considerably better. I was also able to find the best dosages. I believe that learning what foods (and dosages) make your brain work best is a good way to figure out what foods (and dosages) are best for the rest of your body. For example, after I figured out what amount of flaxseed oil was best for my brain, my gums became much healthier (less inflammation). The new test, which I do more often than the older tests, has made clear that there are all sorts of reliable yet mysterious ups and down in my brain function. I was unaware of this.

I want to find out what happens when other people use the new test. I am looking for a small number of people to do the test at least daily and send me their data at least weekly for at least 3 months. The test requires a computer running Windows 7. The test is written in R (free), but you don’t need to know R to use it. The installation requires details that I will need to handle by talking with you.

To find people to do this, I will use a bidding system. (Giving a program to those who ask for it is a waste of time, I have found.) The questions below ask for two bids: non-refundable and refundable. If you use it as promised — you set the details of how much you will use it — you get back the refundable amount.

If this interests you, please apply by sending an email to try.brain.tracking (at) gmail.com with answers to the following questions (as email text, not attachment):

  1. Name, age, sex, location, job.
  2. Computer you will use it on (e.g., Thinkpad 520), age of computer, operating system.
  3. Phone number (and Skype id, if any). I need to talk to you to set it up.
  4. Website or blog (if any).
  5. Any relevant expertise or experience? (e.g., work with computers, researcher, other self-tracking)
  6. Non-refundable amount. How much (U.S. dollars) are you willing to pay (via PayPal) to get this test?
  7. Over 3 months, on what fraction of days will you commit to doing the test at least once? at least twice?
  8. Refundable amount. This money will be refunded if you meet the goals you set in Question 7 and send me the data at least 6 times (spaced at least one week apart).
  9. Anything you want to add?

You will get an automated reply. After that, I will contact you only if I want more information or if yours is one of the winning bids.