Category: personal science

Science in Action: Unexplained Changes in Brain Speed

Seth Roberts6 Comments

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.

 

Lack of Repeatability of Cancer Research: The Mystery

Seth Roberts14 Comments

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.

Does Kerrygold Butter Improve HDL and LDL?

Seth Roberts5 Comments

More: Greg used Kerrygold butter in the results given below. I now see that he omitted data from other butters that did not agree with his conclusions. This makes his results considerably more doubtful and his whole post (in which Kerrygold butter is called “butter”) misleading. I have changed the title of this post to reflect this.

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.

The first five measurements are from lab tests. The rest are from his home machine.

I asked Greg for details.

I’m 36. I bought the cholesterol meter last July after my doctor said he couldn’t figure out why my numbers were a bit high. We both agreed it was not something to worry too much about and that there was no point charging my insurance company for a VAP test every 6 months. We both also agreed that going on a statin was a bad idea. I picked up the meter out of curiosity. I had previously been monitoring my blood sugar (since 2009) and found it to be very interesting, so I thought I could have some fun with the numbers. The result is all the more surprising because I did not expect it. I was tracking my numbers around the time of the experiment [with butter] to make sure they did not go the wrong way like everyone says they should.

The machine is a CardioChek PA [about $600], which is designed for use in doctors offices, not for the consumer market. The device is “CLIA-waived”, which means that the FDA considers it so simple that the user does not need any special training in clinical chemistry (home glucometers fall into the same category). The machine gives significantly different numbers for different people, suggesting it is measuring something real and not spitting out random numbers.

I asked what the reaction to this data has been.

Most people I’ve spoken to have been receptive to the idea [that butter improves blood lipids], but I got no sense that they would be willing to try it for themselves. Most people I know seem to be quite willing to accept the fact that the old stories about cholesterol are not true. In contrast, one conservative cardiologist said I must have “unique genetics”.

Ten Years of Weights, Including Two Years on the Shangri-La Diet

Seth Roberts8 Comments

Here’s a new graph I’ve made of Alex Chernavsky’s data. In 2001, he started weighing himself and recording his weight with the hope that it would help him lose weight. His data shows several interesting things:

1. Long walks really helped. The walks lasted 1.5-2 hours. They weren’t sustainable but the weight loss they caused lasted a remarkably long time — years, apparently, in the sense that it took years to regain the lost weight.

2. A low-carb diet worked well, but only at first. Alex lost a lot of weight initially but then started to regain it. Just before he became vegetarian, he was regaining weight quickly. I don’t know if this is typical. The popularity of low-carb diets has not been matched by availability of data about long-term effects, where by “long-term” I mean four years. Even though low-carb diets are 150 years old (Banting wrote in 1863).

3. The Shangri-La Diet is working better than other alternatives. There’s a difference between (a) showing that a diet causes weight loss and (b) showing that it works better than other ways of losing weight. In this comparison, it appears more sustainable than long walks and the weight loss it causes appears more sustainable than the weight loss from a low-carb diet.

Alex originally used Shangri-La Diet principles by ingesting 4 tablespoons of flaxseed oil washed down with water. (Details here.) He lost weight but then started to slowly regain it. I suggested he increase his intake of flavorless calories so he started to eat 1 tablespoon of coconut oil (about 100 calories) each day with his nose clipped. He stopped slowly gaining weight.

I asked Alex why he has persisted weighing himself so long. He replied:

I had at best a vague idea of what I wanted to do with the data. When I was in graduate school [in neuroscience], I enjoyed plotting the results of my experiments, so I thought it would be fun to have a dataset that consisted of my own weight measures. After I started the SLD, I had a more-concrete reason why I needed to collect the data. I explicitly set out to test the diet.

 

 

The Value of Moodscope

Seth Roberts4 Comments

In 2007, Jon Cousins started tracking his mood to help NHS psychiatrists decide if he was cyclothymic (a mild form of bipolar disorder). After a few months of tracking, he started sharing his scores with a friend, who expressed concern when his score was low. Jon’s mood sharply improved, apparently because of the sharing. This led him to start Moodscope, a website that makes it easy to track your mood and share the results.

I was curious about the generality of what happened to Jon — how does sharing mood ratings affect other people? In January, Jon kindly posted a short survey about this. More than 100 people replied.

Their answers surprised me. First, in a survey about sharing your mood — not about tracking your mood — most respondents did not share their mood. It is as if, in a survey about being tall, most respondents were not tall. Second, although Jon’s mood sharply rose as soon as he started sharing, this was not the usual experience. Sharing helped, some people said, but other people said sharing hurt. For example, one person said her mood was used against her in arguments. Finally, the respondents gave all sorts of persuasive reasons that rating their mood helped them. To me, at least, the value of mood rating isn’t obvious. I can list a dozen hypothetical benefits but whether they actually happen is unclear to me. I rated my mood for years and did it only to learn about the effects of morning faces. MoodPanda, another mood-rating site, gives a few brief vague unenthusiastic reasons to track your mood. And their site is all about mood rating.

In contrast, Moodscope users were clear and enthusiastic about the value of tracking. Here are some reasons they liked mood-tracking:

It is useful to look back sometimes to help you find ways of ‘keeping up’ a positive mood/outlook.

My mood range has definitely narrowed since starting mood stabilizers, so using Moodscope has given me solid evidence that the treatment is working well. I also run statistical analyses of my mood charts against variables like sleep, medication use, and alcohol consumption. The correlations were not particularly meaningful using a 9-point Likert-like scale from a standard mood chart. When I used my Moodscope scores instead, I suddenly found that some of the correlations are (ridiculously!) statistically significant, which also made me feel more certain about what I need to do and change to better manage my mental health.

I could express my miserableness in total safety, without leaning on anybody else. It has proved wonderful. My profile has risen from a score of 7 on day 1 (11 months ago) to the 90s now. Being able to track my reasons for feeling better or worse has been part of this. The patterns are visible, ditto the triggers that send me up or down.

The great benefit of Moodscope has been to confirm the advantages of my own lifestyle management for coping with bipolar disorder. It has shown that what I felt was bad for me, is indeed bad, and what I felt was good for me, is indeed good. (I know that I have to take the meds.)

It helps that I can post things about sleep hours in the comments and see the correlation to the chart.

I have found the tool immensely helpful in gaining insight into how my own behaviour and thoughts can impact upon my mental health. I have gained more control.

It helps me to gain insight into my moods, take responsibility for them and steer a calmer, more productive course through life.

It allows me not to panic when I am low as I can see that ups and downs are all part of life.

Pre-Moodscope, I would not realize i was on the way down until 10 or so days had passed, and so I had done nothing. But with Moodscope, I can see if it’s a trend and do something immediately. It means I deliberately intervene earlier.

I use my scores, and comments, to understand what triggers my low mood and take steps to stop it getting lower, in so far as I am able.

I view it as a diary of sorts, private for my own contemplation.

I want to catch myself before I make a deep plunge and stay down too long. I do use the info with my doctor. I love having something concrete to show and talk about.

It has helped me feel like there is a greater safety net there, and given me a greater awareness of when I’m slipping back into my treacle pit; I now know that any score between 20 and 30 means I am in dangerous territory and need to take some remedial action, and if I get below 20 then I’m really in a bad way.

Moodscope has helped me identify incidents in my life with my mood. For example if I have to assert myself strongly with someone, I feel exhilarated and very proud of myself for about two day then gradually my mood will lower and a week later I will feel apathetic and down. I love that it is helping me make sense of my emotions and as a result I am not judgmental of them.

I’ve found Moodscope really useful in finding out what influences my moods. I am bipolar and after 20 years on lithium I’m managing without any meds. Don’t worry, I came off it slowly, under medical supervision!

I use Moodscope as a sort of diary of how I am feeling. Looking back I can see what really pushed my mood down and oddly it’s not always the major things that you’d imagine. In my case depression is brought on more by physical health problems – I am a CFS sufferer.

I sum up their reasons like this: 1. Helps understand causality (what causes mood to be low or high?). 2. Immediate guidance (should I take action to raise it?). 3. Self-expression (similar to diary). 4. Reassurance (low moods are “part of life”). Alexandra Carmichael wrote about the value of mood-tracking and mood-sharing. Her experience did not repeat Jon’s: She found little initial benefit of sharing, but great eventual benefits (“a kind of deep, healing therapy”). This was the main benefit of tracking for her — that it allowed this sharing. Kari Sullivan also tried Moodscope. She didn’t share her mood. The benefits she list fall under the heading of Reason #1 (helps understand causality). For example, she learned “most social interaction lowers my mood,” which surprised her.

Not everyone liked tracking:

My girlfriend . . . stopped using Moodscope. In her words, “I don’t want Moodscope to remind me how terrible I’m doing.”

She has now decided to give up on taking the test as it just reinforces her feelings of general greyness and sometimes despair.

At a website devoted to collecting new ideas about health, Moodscope ranked #1 out of about 500 ideas.

When I started my self-experimentation I didn’t get anywhere for a long time (after initial success with acne). After 1990, however, I was astonished at the progress I made. One useful discovery after another — how to lose weight, sleep better, be in a better mood, and so on. Over the next 20 years, I improved my health considerably more than all the other scientists in the world put together. I came to see what was happening as a kind of catalysis. The useful information was already there; my personal science was the catalyst that turned it into something useful. (Lack of people like me was why the discoveries were so abundant — a counter-example to Tyler Cowen’s lack-of-low-hanging fruit explanation for stagnation.) Professional scientists were too restricted in what they did.

The Moodscope story is similar. Psychologists have been studying and measuring mood for a long time. The Profile of Mood States is an important result of their research. But no psychologist saw it as an agent of change. It was simply a research tool, albeit a popular one. Only when Jon Cousins started using it for his own selfish purposes did it become clear how useful it could be. He was the catalyst.

Both my story and Jon’s are examples of what I say about DIYization of science: It gets tools into the hands of a larger and more diverse group of possible innovators, who are less “stuck” — less committed to old ways of doing things — than the professionals. They are also more motivated to do something useful than the professionals, who are weighed down with other big concerns — about status, job security, money, and so on.

Personal Science and Varieties of DIY

Seth Roberts2 Comments

How does personal science (using science to solve a problem yourself rather than paying experts to solve it) compare to other sorts of DIY?

Here’s an example of personal science. When I became an assistant professor, I started to wake up too early in the morning. I didn’t consider seeing a doctor about it for several reasons: 1. Minor problem. Unpleasant but not painful. 2. Doctors usually prescribe drugs. I didn’t want to take a drug. 3. Sleep researchers, based on my reading of the sleep literature, had almost no idea what caused early awakening. They would have said it was due a bad phase shift of your circadian rhythm. They often used the term circadian phase disorder but never used the term circadian amplitude disorder — apparently they didn’t realize that such a thing was possible. I decided to try to solve the problem myself — an instance of DIY. Except that, if I made any progress, that would be better than what the experts could provide, which I considered worthless.

There are thousands of instances of DIY, from fixing your car yourself to sewing your own clothes to word processing. Here is one dimension of DIY:

1. Quality of the final product. Better, equal, or worse to what you would get from professionals. Richard Bernstein’s introduction of home blood glucose testing led him to much better control of his blood glucose levels than his doctors had managed. Same as my situation: DIY produced acceptable results, the experts did not.

In contrast to Bernstein, who reduced his blood glucose variability within months, it took me years to improve my sleep. That is another dimension:

2. Time needed. Personal science, compared to other DIY, is orders of magnitude slower.

Here are some more dimensions:

3. Training needed. I don’t know how much training personal science requires. On the face of it, not much. I had acne in high school. I could done self-experimentation at that point. It just didn’t occur to me. On the other hand, I think effective personal science requires wise narrowing of the possibilities that you test. For most health problems, you can find dozens of proposed remedies. How wise you need to be, I don’t know.

4. Commercialization. Some forms of DIY are entirely the creation of businesses — cheap cameras, home perms, IKEA, etc. Bernstein’s work happened because of a new product that required only a drop of blood. The company that made it wanted doctors to do DIY: measure blood glucose levels in their office (fast) rather than having the measurement made in a lab (slow). When I started to study my sleep, no business was involved. Now, of course, companies like Zeo and the makers of FitBit want users to do personal science.

5. Price. My sleep research cost nothing, which in the DIY world is unusual. The term DIY is almost entirely a commercial category: Certain books and goods are sold to help you DIY.

6. Customization possible. Some kinds of DIY give you the tools to build one thing (e.g., IKEA, home perms). Other kinds (e.g., Home Depot, word processing) give you the tools to build a huge range of things. This dimension is variation in how close what you buy is to the finished product (Ikea = very close, word processing = very far). Personal science allows huge customization. It can adjust to any biology (e.g., your genome) and environment (your living conditions).

7. Benefit to society. If I or anyone else can find new ways to sleep better — especially safe cheap easy ways — and these solutions can be spread, there is great benefit to society, by comparison to DIY that allows non-professionals to reproduce what a professional would create (e.g, IKEA).

You might say that personal science isn’t really DIY because, compared to other DIY, (a) it is much slower and (b) the potential benefit to society is much greater. But those features are due to the nature of science. Any form of DIY has unique elements.

My mental picture of DIY is that there are two sides, producers and consumers, and in many domains (health, car maintenance, word processing, etc.) they creep toward each other in the sense that what producers can make slowly increases and what consumers are capable of slowly increases. When they meet, DIY begins. In some cases, the business has done most of the changing; the DIY is very easy (e.g., Ikea). In other cases, the consumer has changed a lot (literacy — not easy to acquire). Either way, the new DIY causes professionals who provided that service or good for a living to lose business.

The DIYization of Beer Brewing and Innovation

Seth RobertsLeave a comment

The key point — as far as I’m concerned — in this article about the DIYization of beer brewing comes in the middle of a paragraph:

Home brewing is part of a broad spectrum of DIY activities including amateur astronomy, backyard biodiesel brewing, experimental architecture, open-source 3-D printing, even urban farming. . . . Many of these pastimes can lead to new ideas, processes, and apparatus that might not otherwise exist.

Likewise with the DIYization of science: It will produce new ideas, solutions, etc. The Shangri-La Diet is an example.

Thanks to David Archer.

One Doctor’s View of Personal Science (more)

Seth Roberts17 Comments

A few weeks ago I blogged about a leukemia doctor’s disapproval of self-experimentation (“you won’t learn anything and others won’t learn from it, either”). What I wrote was reposted at The Health Care Blog, where it elicited this comment (by “rbar”):

Sigh. Mr Roberts did it again, he simply does not (want to) understand that anecdotal evidence is of little value (let me give you an example: I self experiment with traffic signals; I noted that I can considerable cut down on travel times when ignoring red lights and stop signs; there are no drawbacks whatsoever, no one get hurts, and even my gas mileage/carbon footprint got better) .

Individuals who have similar questions as Mr. Roberts should look up the following key words, because they may understand why controlled studies are far superior to anecdotal evidence:
-placebo effect
-regression to the mean
-misattribution error [apparently rbar means error in determining the cause of a change]-self limited conditions/natural fluctuation of chronic conditions
-and in terms of drawbacks of experimentation: primum non nocere, and also the fact that anecdotal evidence adds relatively little to humanity’s knowledge base

Does all that mean that patients should not be well informed, active and making suggestions to their treating physicians? Of course absolutely not. Being knowledgeable about one’s condition is different from self experimentation. Is that intellectually challenging?

One reply to this comment said we should be aggregating data across patients. “I believe Mr. Roberts is alluding to the power of aggregating real-world data across patients to generate insights into what may and may not work, not to giving undue weight to any single anecdotal case.” No, I was looking at it from the point of view of the self-experimenting patient. If you have a health problem, and you can measure it often (daily, weekly) you can find out what works faster than your doctor — often much faster. You can test many more possible solutions. This is what Richard Bernstein taught the whole world of diabetes, starting in the 1960s, when he pioneered home blood glucose testing. Apparently rbar also objects to that.

Rbar’s comment is dismissive (“Sigh”, “Is that intellectually challenging?”) and partly obscure (“ignoring stop signs and stoplights” — huh?). Because patients who self-experiment may make “misattribution errors” they shouldn’t self-experiment? That’s like saying because people may make reasoning errors they shouldn’t reason.

The true meaning of rbar’s comment may be hidden in his statement that it’s okay for patients to “make suggestions to their treating physician.” Which shows who he thinks should be boss in the doctor-patient relationship. When a patient self-experiments, the doctor is no longer boss. Maybe rbar is a doctor. Maybe he feels threatened by self-experimentation. If so, I hope he’s right.

More A later reply to rbar put it well: ” Your list of possible pitfalls . . . is similar to lists I remember seeing back in graduate school in various research handbooks. I do not see how you go from the fact that these effects and errors are possible to the conclusion that the whole endeavor isn’t worthwhile.”

 

 

DIYization: The Word I Was Looking For

Seth Roberts1 Comment

In a recent post I wondered what’s a good word to describe the next step in economic progress after specialization — when making/doing X is done by the general public (not as a job) instead of just by paid specialists (as a job). For example, the introduction of cheap cameras allowed the general public, not just professional photographers, to take pictures. Personal science is an example of such a shift, of course. Thank you for your many suggestions, such as laitization, deguilding, promethization, and several more. The combination of Keimpe Wiersma’s suggestion (DIY) and wobbly’s suggestion (deguilding) led me to DIYing and DIYization.

DIYing, I learned, is an existing word with a different meaning (to do DIY). Although ordinary DIY (Home Depot) is associated with men, women appear to use DIYing far more than men and they use it to describe traditionally feminine activities (see this). For example, there is a blog DIYing To Be Domestic by a woman. This is irrelevant to whether I use it — it’s just interesting.

DIYization is much rarer. It appears in a 2005 essay called “Scandinavian Dreams: DIY, Democratisation and IKEA” where it refers not to a change in an activity but to a change in society — toward more DIY. IKEA, says the essayist, is an example of “the DIYization of society.”

DIYing is shorter. DIYization is more self-explanatory, less likely to be confused with dying, and makes clearer the connection with specialization. Not to mention it is more pompous — more Veblenesque. In the last chapter of The Theory of The Leisure Class, Veblen used long rare words to say that academics show off their uselessness using by using long rare words.

What Is a Good Word For This?

Seth Roberts45 Comments

Can you help me? I am looking for a word — maybe a new word — to describe the transformation of an activity from (a) something done only by trained specialists, as part/all of their job to (b) something done by the general public, not as a job. For example:

  • word processing software has made producing an attractive manuscript something that you no longer need hire a secretary to do — you can do it yourself.
  • digital cameras and software have made producing high-end photographs something you no longer need a professional photographer to make.
  • When I was a graduate student I hired a professional to make publication-quality figures for my scientific papers. Now I make them myself.

The transition I am talking about is part of a longer historical sequence that goes like this:

  1. Hobby
  2. Part-time job
  3. Full-time job
  4. Specialization (= division of labor)
  5. [new word goes here]

The best word I can think of is deprofessionalization. Unfortunately that has been used with a different meaning. Amateurization doesn’t work because amateur often means hobbyist. Popularization doesn’t work because the status of the activity has changed — from something done as part of a job to something done not as a job. It is one of several ways a job can change:

  • More efficient. New tools, materials, etc., make it possible to do the same job in a shorter period of time or at lower cost.
  • Higher quality. New tools, etc., make it possible to do a better job.
  • More exclusive (= higher barriers to entry). Something (e.g., licensing requirements) makes it harder for others to compete with you.
  • Less exclusive. Something (e.g., the Internet) makes it easier for others to compete with you.
  • ???. People no longer need to hire you or someone like you to do what you do. They do it themselves.

I care because personal science (science done to help oneself) is an example. For a long time, non-trivial science was done only by professional scientists. Now it is being done by non-professionals.

More What about publicization? Or is it too ugly? I looked up democratization as a possibility but found this under “democratization of photography”:”Serious photography has gone from being the preserve of the reasonably well off to something that just about anyone can take up with minimal expense”. That isn’t what I mean here — that the price of something comes down. Hoipolloization is too long. What about massification?

Still More It really is DIY, I hadn’t thought of that. That exactly conveys the transition from job to non-job. DIYing (or should it be DIYization?) has a nice ring to it, is very short, is not pompous, and would not need to be defined. I also like promethization, deguilding, democratization, and deprofessionalization.