Health

Is R0 < 1 yet?

Posted by Peter on April 14, 2020
Posted in: Health. Tagged: , , .

I recently made a bet with Robin Hanson that US COVID-19 deaths will be less than 250,000 by Jan 1, 2022 (details hiding in these Facebook comments).

I gave a few hints here about my reasons for optimism (based on healthweather.us). I’ll add some more thoughts here, but won’t try to fully explain my intuitions. Note that these are more carefully thought out than my reasoning at the time of the bet, and the evidence has been steadily improving between then and now.

First, a quick sanity check. Metaculus has been estimating about 2 million deaths from COVID-19 worldwide this year. It also predicts that diagnosed cases will decline each quarter from this quarter through at least Q4 2020, and stabilize in Q1 2021 at 1/10 the rate of the current quarter, suggesting that most deaths will occur this year.

U.S. population is roughly 4% of the world, suggesting a bit over 80k deaths if the U.S. is fairly average. The U.S. looks about a factor of 5 worse than average as measured by currently confirmed deaths, but a bit of that is due to a few countries doing a poorer job of confirming the deaths that happen (Iran?), and more importantly, the Metaculus forecasts likely anticipate that countries such as India, Brazil, and Indonesia will eventually have a much higher fraction of the world’s deaths than is the case now. So I’m fairly comfortable with betting that the U.S. will end up well within a factor of 3 of the world per capita average.

I was about 75% confident in late March that R0 had dropped below 1, and my confidence has been slowly increasing since then.

Note a contrary opinion here. It appears to produce results that are slightly pessimistic, due to assuming that testing effort hasn’t increased.

Yet even if it’s currently a little bit above 1, there’s still a fair amount of reason for hope.

Many people have been talking as if strict shelter-in-place rules (lockdowns) are the main tools for keeping R0 < 1. That’s a misleading half-truth. Something like those rules may have been critical last month for generating quick coordination around some drastic and urgent changes. But the best longer-term strategies are less drastic and more effective.

One obstacle to lowering R0 is that hospitals are a source of infection. I’m pretty sure that will be solved, on a lousy schedule that’s unconnected with the lockdowns.

Within-home transmission likely has a significant effect on R0. Lockdowns didn’t cause any immediate drop in that transmission, but that transmission drops a good deal as the fraction of people who have been staying at home for 2+ weeks rises, so R0 is likely declining now due to that effect.

Most buildings that are open to the public should soon require good masks for anyone to enter. It wasn’t feasible to include such a rule in the initial lockdown orders, but there’s a steady move toward following that rule.

I expect those 3 changes to reduce R0 at least 20%, and probably more, between late March and late April.

Robin is right to be concerned about the competence of institutions that we relied on to prevent the pandemic. Yet I see modest reasons for optimism that the U.S. will mostly use different institutions for test and trace: Google, Apple, LabCorp, etc., and they’re moderately competent. Also, most institutions are more competent at handling problems which they recall vividly than they are at handling problems which have been insignificant in the lifetimes of most executives.

We can be pretty sure based on China’s results that R0 < 1 is not a narrow target. Wuhan got R0 lower than the key threshold by a factor of something like two. They did that in roughly the worst weather conditions – most of the time, warmer (or occasionally colder) weather will modestly reduce R0. So we’ll be able to survive a fair amount of incompetence.

But there’s still plenty of uncertainty about whether next week’s R0 will be just barely acceptable, or comfortably below 1.

Deliberate Infection?

The challenges of adapting to the most likely scenarios took nearly all of my attention in March. So I had no remaining slack to adequately prepare for a scenario that looked unlikely to me, but which looked likely to Robin. For one thing, I ought to have evaluated the possibility that money will be significantly more valuable to me if Robin wins the bet than if he loses.

It is certainly possible to imagine circumstances where deliberate coronavirus infection is quite valuable. But it looks rather low value in the scenario I think we’re in.

I don’t have much hope of getting a sensible program of deliberate infection in a society that couldn’t even stockpile facemasks in February.

I also see only a small chance that talking about deliberate infection now will help in a future pandemic. I expect this to be humanity’s last major natural pandemic (note: I’m too lazy today to evaluate the relevance of bioterrorist risks). I don’t know exactly how we’ll deal with future pandemics, but the current crisis is likely to speed up some approaches that could prevent a future virus from becoming a crisis. Some conjectures about what might be possible within a decade:

  • Better approaches to vaccination, such that vaccines could become widely available within a week of identifying the virus.
  • Medical tricorders that are as ubiquitous as phones, and which can be quickly updated to detect any new virus.

Still, I do think deliberate infection should be tried in a few places, in case the situation is as desperate as Robin believes. I’ll suggest Australia as a top choice. It has weather-related reasons for worrying that the peak will come in a few months. It has substantial tuberculosis vaccination, which may reduce the death rate among infected people by a large margin (see Correlation between universal BCG vaccination policy and reduced morbidity and mortality for COVID-19: an epidemiological study).

Note that tuberculosis vaccination looks a good deal more promising than deliberate infection, so it should be getting more attention.

Other odds and ends

Some of the concerns about a lasting economic slowdown are due to expectations that the restaurant industry will be shut down for years. I expect many other businesses to reopen within months with strict requirements that everyone wear masks, but it’s rather hard to eat while wearing a mask. So I see a large uncertainty about which year the restaurant business will return to normal. Yet I also don’t see people who used to rely on restaurants putting up with cooking at home for long. I see plenty of room for improvement in providing restaurant-like food to the home.

Current apps for delivery from restaurants seem like clumsy attempts to tack on a service as an afterthought. There’s plenty of room to redesign food preparation around home delivery, in ways that more efficiently and conveniently handle more of the volume that restaurants were handling before.

We have significant unemployment among restaurant workers, combined with food being hard to acquire for reasons which often boil down to labor shortages (combined with rules against price gouging). That’s not the kind of disruption that causes a lasting depression. The widespread opposition to price gouging is slowing down the adjustments a bit, but even so, it shouldn’t be long before the unemployed food service workers manage to become redeployed in whatever roles are appropriate to this year’s food preparation and delivery needs.

Finally, what should we think about this news: SuperCom Ships Coronavirus Quarantine Compliance Technology for Immediate Pilot?

Nutrient Power

Posted by Peter on April 11, 2020
Posted in: Book Reviews, Health.

Book review: Nutrient Power: Heal Your Biochemistry and Heal Your Brain, by William J. Walsh.

Nutrient Power is an eccentric book about nutritional problems and their effects on the brain. It’s full of information that’s somewhat at odds with conventional wisdom.

It’s a short book, and I wasn’t tempted to read all of it. I usually don’t review books unless I’m willing to read the whole thing, yet this time I can’t resist the temptation.

I expect that it’s important reading if you’re building your own model of how nutrition affects cognition, you’re frustrated about how little you’ve found in peer-reviewed publications, and you’re interested enough to treat this as something closer to a career than a hobby. If, like me, you’re less ambitious than that, you should expect to find at least parts of the book frustrating. And if you just want easy-to-follow or rigorously proven advice, this is definitely not the book you want.

I’ll guess that a bit more than half of the unusual ideas are correct and valuable, and that less than 10% of the others are harmful. Don’t expect it to be easy to distinguish the good ideas from the bad.

Continue Reading

Some COVID-19 Notes

Posted by Peter on March 22, 2020
Posted in: Health, U.S. Politics. Tagged: .

Some links to information sources that I’ve been using:

Food delivery is erratic in Berkeley. GoodEggs seems to have major food shortages, and maybe some labor shortages. Model Meals has been working almost as smoothly as normal, providing I place my order a day before their deadline – they are selling out of most things near their deadlines. I tried Instacart for the first time, and it seems substantially degraded by high demand – I had problems with getting 2 apples when I ordered 2 3-lb bags of apples (no that wasn’t listed as a substitution – the intentional substitutions worked fine). I’m guessing I’ll want to go back to shopping at grocery stores in person in a week or so. Infection rates are almost certainly dropping here now that the shelter-in-place rules have been around for a while, but it will likely be a week before much evidence confirms that.

I hiked in Briones Regional Park on Friday. I expect to see no more than 5 cars at the trailhead on a weekday; this time there were more than 30! People seemed unusually friendly. Most were making a decent effort to keep a 6 foot distance from me, but a few of the younger ones seemed to not care.

I think OPEC just collapsed, and nobody celebrated. I suppose the climate change implications might be a bit bad, but most effects will be pretty good.

Will auto sales be up or down a year from now? Loss of wealth will delay some purchases, and a fair number of existing drivers will drive less. But some people will switch from public transport to owning a car; others will switch from UberPool to UberX.

A modest number of maids will be replaced by Roombas [disclosure: I just bought stock in iRobot].

Politicians are talking about bailing out airlines, with terms that prevent them from stock buybacks. I expect that restriction to be purely symbolic – it will be a while before airlines are tempted to do buybacks anyway. If politicians were really upset about buybacks, they would instead deny the bailout to a single airline that was the most reckless in buybacks (maybe the one that achieved the worst debt to tangible equity ratio? I think that’s Delta). Alas, politicians won’t do that. After all, it might help people see that bailouts are somewhat targeted at helping bond and stock holders, and that the planes, workers, etc., don’t just vanish in the (somewhat unlikely) event that bankruptcy proceedings cause one company to shut down.

Some senators are under fire for insider trading on some sort of COVID-19 insights. If they profited from improved analysis of public information, I think that’s great! I’d like them to have an incentive to listen to experts. It would be suspicious if they profited from secret data, but I can’t find much reason to think that’s what happened – as far as I can tell, the relevant evidence was made public fairly quickly, and what mattered was competent evaluation of that evidence. And the most important question is what else they did to prepare. If, as the news storytellers vaguely imply, they did little else to warn people, then either they were more confused than the reports suggest, or they were recklessly negligent.

Shutting borders can hurt:

One issue has been restrictions on travel intended to stem the spread of coronavirus, which has affected [U.S. ventilator maker] ResMed’s Singapore factory which employs many workers from neighbouring Malaysia. He said ResMed has appealed to the Malaysian government for an exemption so its workers can travel to Singapore.

Biomerica has a new COVID-19 test with some apparently nice features that differ from the common PCR-based tests. However:

Biomerica is positioned to begin filling large international orders of this disposable one-use tests within weeks, assuming international product shipping channels remain open and active.

In addition, Biomerica has begun the application process with the FDA under the COVID-19 Emergency Use Authorization (EUA), aimed at the possible clearance and eventual use of the test in the US. At this time, the product is not available for sale or use in the US.

And finally, some related entertainment about flattening the curve of armchair epidemiology.

Oura

Posted by Peter on February 16, 2020
Posted in: Health. Tagged: , , .

I’ve been using an Oura sleep tracking ring for six months.

In some ways it’s an impressive piece of technology. It’s small enough to not distract me much, and they went overboard in making the user interface simple. Simple, as in there basically aren’t any controls. I just put it on my finger, and occasionally put it on the charger.

Yet it does a poor job of what I expected it to do: track how long I sleep. It occasionally thinks I’m in bed when I’m not wearing it. If I get up to use the bathroom, it’s hard to predict whether it will decide that’s the start or end of my time in bed.

But the Oura reminded me that “8 hours of sleep” isn’t a good description of what I want – that’s just a crude heuristic for “slept well enough that further sleep won’t improve my productivity / health”. The Oura observes other relevant evidence: body temperature, breathing rate, heart rate, and heart rate variability. I.e. things I ignored because they were too hard to evaluate, rather than because I decided they weren’t important.

If I did a strenuous hike yesterday, it will tell me that 7.5 hours of sleep wasn’t enough, whereas if I’d spent yesterday relaxing, it might have told me that 7 hours was plenty, and that I should be ambitious.

It’s somewhat obvious that I need more sleep when a cold raises my body temperature. The Oura convinced me that there’s a much more general pattern of above average body temperature indicating an increased need for sleep.

I’ve tried comparing the Oura’s heart rate variability measurements with those of the emWave2, and I couldn’t see much correlation. I’m inclined to trust the emWave2 more, but I’m not aware of good evidence on the subject.

The Oura also helps track exercise, at least for hiking (it doesn’t seem to do much for weightlifting, but most of my exercise comes from walking/hiking). It reports slightly less calories burned than what I calculate from a cheap Garmin GPS and this calculator. I’m unsure which of those 2 measures is more accurate. If I were only using the GPS to measure calories burned, I’d give up on the GPS, because the Oura doesn’t have problems such as poor reception, or me forgetting to turn it on or off at the start and end of a hike.

It said I slept 3 hours on a red eye flight. My subjective impression was that it was somewhat debatable whether any of that ought to be classified as sleep. But what do I know? I have some evidence that I can sleep without being aware of sleeping (mainly from people reporting that I was snoring, at a time when I thought I was awake and not snoring).

My ring isn’t quite the right size for my ring finger. I ordered it based on prior information about what ring size worked for me, rather than using Oura’s measuring procedure. I’ve ended up wearing on the middle segment of my middle finger instead. That’s works well enough that the difference seems unimportant.

See this comparison with several alternatives for a more detailed analysis.

Mostly, the Oura simply reassured me that I don’t have significant sleep problems, other than the times when it’s obvious that I took too long to fall asleep, or woke up too early. I suspect that the Oura would have been moderately valuable if I had had sleep problems that were hard for me to detect.

Move Your DNA

Posted by Peter on January 28, 2020
Posted in: Book Reviews, Health.

Book review: Move Your DNA: Restore Your Health Through Natural Movement, by Katy Bowman.

Move Your DNA does for physical activity what paleo diet advice does for food.

The book is full of suggested movements to practice, making it look somewhat like a yoga book.

Bowman criticizes the common notion of exercise, because it leads to people repeating a tiny set of motions.

Most of us wouldn’t imagine that we had a healthy diet if we ate nothing but carrots, or nothing but liver, even though eating more of those is usually a good idea. Yet plenty of people seem to imagine that they can offset the risks of spending 60 hours per week in chairs by running for a few hours on a carefully maintained surface, repeating a single type of motion with no variation.

A healthier lifestyle would include a wide variety of motion, ideally motivated by the need to accomplish a wide variety of tasks such as carrying wood, digging, pounding nuts, and walking on terrain with lots of little irregularities (she calls this cross-terraining).

How much does it matter? Bowman provides surprising hints, and good theoretical reasons for concern, but leaves me with a good deal of uncertainty about the magnitude of the harm.

Continue Reading

Baze

Posted by Peter on December 29, 2019
Posted in: Health. Tagged: .

Convenient, affordable blood tests seem to be important tools for improving health. See my review of The End of Alzheimer’s for hints about why they’re important.

Talking20 and Theranos raised some hopes, then they failed.

Now comes Baze. They shipped me a device that I pressed against my arm. I waited a few minutes, took it off, and shipped it back. I was a bit uncertain about my ability to read the light that changed color to indicate the device had collected enough blood, but I seem to have gotten it right.

Half the time that it took to complete my test involved walking to the nearest FedEx drop box, which is a good deal closer than the nearest LabCorp or Kaiser lab. I had no need to worry about unpredictable delays waiting for a technician to be available to extract my blood.

I got 10 nutrient levels tested for a sale price of about $50. Many of those tests aren’t available on privatemdlabs.com, and the ones that are available are around $50 per nutrient. Life Extension has more of the tests, including Selenium (list price $88, but I normally wait for their spring sale), and Omega-3: $79 for a test that requires me to extract blood from my finger on my own. I had trouble getting enough blood that way, and never got a result, presumably because I didn’t do it well enough. So if I tried to test those 10 nutrients without Baze, I’d have paid maybe $500 and only gotten 7 or 8 results.

Are Baze’s results accurate? I’ve been tested for several of the nutrients previously, and the Baze results for those are similar enough to be reassuring. Their technology seems to have a decent pedigree.

So far, it sounds almost too good to be true. Is there a catch? Maybe. Baze does have a business model that makes me a bit nervous.

Baze is part of Nature’s Way, and tests nutrients in part in order to sell us vitamins in order to correct any deficiencies that it detects.

That does bias Baze away from providing the tests that are most valuable for influencing health-related decisions.

It also biases Baze toward recommending more supplements than is optimal. I don’t see any clear signs that they’re erring in that direction. I also see a distinct shortage of strong arguments in favor of their recommendations.

For vitamin D, they classified my level of 58.3 as excessive, when it’s only about 10% above the level I was aiming for, and there are many people advocating higher levels. That’s a clear sign that they’re not pushing too many vitamins on us.

Yet for choline and omega-3, they classified my blood levels as optimal, yet are still sending me those supplements. There’s at very least something wrong with their explanation here. Yet in both cases, I see some plausible arguments from independent sources that my levels are a bit below ideal, and I had been mildly concerned that I wasn’t consuming enough.

Maybe they’ve got a good explanation hiding somewhere on their blog, but the easy-to-navigate parts of their website are written more for people who want simple and convenient answers from a respected authority. Something feels wrong with their attempt to act like such an authority without providing more evidence of competence than I’ve seen.

They’re also sending me vitamin E and magnesium. I’m pretty confident that I’m consuming a bit more than the RDA for both of those, yet my test results say I’m a bit low in both.

I’m concluding that they have not yet given into the temptation to sell too many vitamins, but they’re putting little effort into reassuring me about this.

Their choice of which tests to do reassured me a bit. They test B12 via methylmalonic acid rather than the less sensitive direct test, and they avoid some nutrients that are more risky to supplement (iron, B6, A, calcium).

Potassium is an important nutrient that many people don’t get enough of. Baze doesn’t do anything with potassium, because potassium supplements are heavily regulated, and because low potassium levels can have causes that ought to be treated by doctors.

Fiber is another important nutrient that many people eat too little of. But that’s rather tricky to evaluate via a blood test – insulin resistance measures say something relevant, but it’s hard to quantify the connection, and doing so might raise novel regulatory issues.

With pretty much all of the nutrients that Baze sells, the evidence for benefits from supplementing is underwhelming, resting mainly on correlations. Where I’ve seen RCTs that test supplementing, only vitamin D seems to show a clear benefit.

I hope Baze focuses more on increasing the variety of biomarkers that it tests for, and less on selling vitamins. I would like to use them for more testing, but not for getting more vitamins. Optimizing our vitamin pill consumption is far from the most valuable goal that this new technology can accomplish.

I suppose the more valuable uses of the technology work best with a fair amount of doctor involvement, and the medical system changes slowly enough that Baze might have needed to introduce the less valuable uses first.

Baze seems good enough now that most people with below-average health (that includes most people over 60) will get a bit of benefit from Baze.

Warning: they report results in different units than I’m used to, so I needed to look up several conversion factors to compare my Baze results to my prior results.

The Paleo Cure

Posted by Peter on December 1, 2019
Posted in: Book Reviews, Health. Tagged: .

Book review: The Paleo Cure, by Chris Kresser.

I wish I had read this when I went paleo 7 years ago. It’s more balanced than the sources I used. Alas, it was published shortly after I finished a big spurt of learning on the subject.

It still has a modest number of ideas that seem new to me, and many ideas that I’d have liked to have known when the book was first published, but which I found through less organized sources.

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Mouse Chow Questions

Posted by Peter on October 6, 2019
Posted in: Health. Tagged: .

[Highly speculative, and rather near the fringes of my expertise].

I’ve previously mentioned that medical studies on mice may have produced poor results due to the use of unnatural environments (cold stress, and the lack of burrow-like protection from predators).

Now I notice that standard rodent food has suspiciously high methionine levels.

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Are Blue Zones Healthy?

Posted by Peter on August 17, 2019
Posted in: Health. Tagged: , .

I’ve mentioned Blue Zones approvingly several times on this blog (here, here, and here).

Alas, there are reasons to doubt that they’re unusually healthy. The paper Supercentenarians and the oldest-old are concentrated into regions with no birth certificates and short lifespans makes a decent case that they’re mostly just areas where ages have been overstated. There are some relatively unhelpful arguments about who’s right on Andrew Gelman’s blog and on Bluezones.com.

As a consequence, I’m slightly decreasing my opinion of some foods that I was encouraged to eat by the Blue Zone memes: whole grains, beans, olive oil, and sweet potatoes. Sweet potatoes still seem likely to be quite healthy compared to the average American food, but I’m now uncertain whether they’re better or worse than the average paleo food (I previously considered them one of the best foods available). The rest of those foods seem no worse than the average American food, but I’m less optimistic about the safety of the average American food than I previously was.

I’ve also become less confident in the safety of a diet with less than 10% of calories from protein (Blue Zone Okinawans in 1949 got 9% of calories from protein), but I’d already decided not to pursue a low protein diet.

I’ve slightly decreased my opinion of Steven Gundry and Valter Longo

H/T William Eden.

The Good Gut

Posted by Peter on July 31, 2019
Posted in: Book Reviews, Health. Tagged: .

Book review: The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health, by Justin Sonnenburg and Erica Sonnenburg.

I had hoped this book would help me improve my gut health. Alas, their advice is of limited value, mostly focusing on changes that I’d already adopted based on other types of nutritional ideas, such as eating more fiber from diverse sources. That limited value is probably due mostly to the shortage of useful research on this subject, rather than to any failing of the authors. Research on these topics seems hard due to the complexity of the microbiome, and the large variation between people.

The book convinced me to eat more kimchi, and left me wondering whether to try consuming more bacteria in pill form.

The book repeats warnings that I’d read elsewhere about the dangers of antibiotics, and the problems that arise from having an insufficiently diverse microbiome, such as autoimmune diseases.

I have been placing heavy emphasis on fiber in my nutritional strategies, while having a gut feeling that the concept of fiber left something to be desired. The book pointed me to an alternative concept: microbiota accessible carbohydrates (MACs), which mostly means carbs that aren’t absorbed by the small intestine. A diverse set of MACs feeds a diverse set of microbiota, which at least correlates with good health.

Alas, it seems impossible to reliably measure MACs by analyzing food in isolation – different people’s small intestines absorb different substances. There are also complications such as erythritol, which is mostly absorbed in the small intestine (and is then removed without doing much), but about 10% of which ends up feeding microbiota in the colon. So I’m still stuck with estimating my MAC consumption via the standard fiber estimates, and taking care to get it from diverse sources.

The Sonnenburgs explain that food preparation affects absorption. Flour is absorbed faster than less-processed grain, and the meaning of “flour” has changed over the past century or so, from something that was ground coarsely and eaten soon after, to something that is ground very fine, and stays on a shelf long enough to go rancid if it is whole-grain flour. That nudged me toward a more nuanced position on grains. The “grains are not food” rule was a simple way to improve my diet, but there are clearly big differences between the best whole grains and the worst grain-derived products.

It also helps me understand how grains, as typically used, gradually morphed into mostly being junk food without an easy way to detect the worst effects. More sophisticated machines to grind the grains led to a texture that was more quickly absorbed, leaving less for microbiota. The switch away from whole grain flour was likely, in part, a gradual adaptation to a system where the flour was ground at an increasingly distance from the home, and became more likely to go rancid if the germ wasn’t discarded.

The book has a section on how infants get a microbiome, which explains why it’s really hard to find or create a good substitute for human milk.

The Sonnenburgs have unusual heuristics about when they wash their hands, designed to reduce pathogens while welcoming good bacteria. They avoid washing after gardening or petting the family dog, but are careful to wash after going to places where they could get germs from many other people – malls, petting zoos, etc.

I’m discouraged by the news that microbiome treatments such as Fecal Microbiota Transplantation (FMT) may be regulated as drugs. It seems like regulations should be modeled somewhat more closely on food, or blood transfusion, regulation. Like food, FMT should have broader goals than just combating specific diseases, should provide diverse inputs, and should bear some resemblance to what naturally enters our bodies. Like blood transfusions, FMT should be reasonably safe unless there’s something unusual about the donor.

The book’s advice overlaps a lot with paleo-like advice to go back to how our ancestors ate, played, etc., with a rather balanced approach to borrowing from our grandparents’ lifestyle versus borrowing from hunter-gatherer lifestyles. The book is solid, often at the expense of being exciting.