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The New Normal

posted by Jason Kottke   Jul 09, 2020

This Is Fine

For Vox, David Roberts writes about how “shifting baselines” affect our thinking and how easily overwhelmingly large issues like climate change or a pandemic can become normalized.

Maybe climate chaos, a rising chorus of alarm signals from around the world, will simply become our new normal. Hell, maybe income inequality, political dysfunction, and successive waves of a deadly virus will become our new normal. Maybe we’ll just get used to [waves hands] all this.

Humans often don’t remember what we’ve lost or demand that it be restored. Rather, we adjust to what we’ve got.

The concept of shifting baselines was introduced in a 1995 paper by Daniel Pauly. Roberts explains:

So what are shifting baselines? Consider a species of fish that is fished to extinction in a region over, say, 100 years. A given generation of fishers becomes conscious of the fish at a particular level of abundance. When those fishers retire, the level is lower. To the generation that enters after them, that diminished level is the new normal, the new baseline. They rarely know the baseline used by the previous generation; it holds little emotional salience relative to their personal experience.

And so it goes, each new generation shifting the baseline downward. By the end, the fishers are operating in a radically degraded ecosystem, but it does not seem that way to them, because their baselines were set at an already low level.

Over time, the fish goes extinct — an enormous, tragic loss — but no fisher experiences the full transition from abundance to desolation. No generation experiences the totality of the loss. It is doled out in portions, over time, no portion quite large enough to spur preventative action. By the time the fish go extinct, the fishers barely notice, because they no longer valued the fish anyway.

And it’s not just groups of people that do this over generations:

It turns out that, over the course of their lives, individuals do just what generations do — periodically reset and readjust to new baselines.

“There is a tremendous amount of research showing that we tend to adapt to circumstances if they are constant over time, even if they are gradually worsening,” says George Loewenstein, a professor of economics and psychology at Carnegie Mellon. He cites the London Blitz (during World War II, when bombs were falling on London for months on end) and the intifada (the Palestinian terror campaign in Israel), during which people slowly adjusted to unthinkable circumstances.

“Fear tends to diminish over time when a risk remains constant,” he says, “You can only respond for so long. After a while, it recedes to the background, seemingly no matter how bad it is.”

Ok, I’ll let you just read the rest of it, but it’s not difficult to see how shifting baselines apply to all sorts of challenges facing the world today. I mean the lines “You can only respond for so long. After a while, it recedes to the background, seemingly no matter how bad it is.” seem like they were written specifically about the pandemic.

Anthony Fauci: USA on Track for 100,000 Covid-19 Cases Per Day

posted by Jason Kottke   Jun 30, 2020

US Covid Stupid Graph

The director of the National Institute of Allergy and Infectious Diseases, Anthony Fauci, told a Senate committee today that the US could be heading towards 100,000 new reported cases of Covid-19 per day. 100,000 cases per day. Yesterday the US recorded about 40,000 new cases.

“It is going to be very disturbing, I will guarantee you that,” he said.

“What was thought to be unimaginable turns out to be the reality we’re facing right now,” Fauci said, adding that “outbreaks happen, and you have to deal with them in a very aggressive, proactive way.”

Fewer than 20 countries have recorded more than 100,000 cases in total. Canada, for instance, has confirmed about 106,000 Covid-19 cases since the outbreak began.

Public health and infectious diseases experts, who have been gravely concerned about the way the U.S. response has unfolded, concurred with Fauci’s assessment.

Bars and restaurants are reopening around the country without any serious effort to test/trace/isolate/support. In the absence of strident guidance from the federal government, people are worrying less about social distancing and wearing masks to protect others. As this guy says, it’s just a matter of math:

“It’s unfortunately just a simple consequence of math plus a lack of action,” said Marm Kilpatrick, an infectious diseases dynamics researcher at the University of California, Santa Cruz. “On the one hand it comes across as ‘Oh my God, 100,000 cases per day!’ But then if you actually look at the current case counts and trends, how would you not get that?”

Absolutely nothing has changed about the virus, so its spread is determined by pretty simple exponential growth.

Limiting person-to-person exposure and decreasing the probability of exposures becoming infections can have a huge effect on the total number of people infected because the growth is exponential. If large numbers of people start doing things like limiting travel, cancelling large gatherings, social distancing, and washing their hands frequently, the total number of infections could fall by several orders of magnitude, making the exponential work for us, not against us. Small efforts have huge results.

We’ve known for months (and epidemiologists and infectious disease experts have known for their entire careers) what works and yet the federal government and many state governments have not listened and, in some cases, have actively suppressed use of such measures. So the pandemic will continue to escalate in the United States until proper measures are put in place by governments and people follow them. The virus will not change, the mathematics will not change, so we must.

Graph at the top of the post via Rishi Desai.

Covid-19 Superspreading Events and “Speech Superemitters”

posted by Jason Kottke   Jun 25, 2020

From Christie Aschwanden’s Scientific American article about How ‘Superspreading’ Events Drive Most COVID-19 Spread comes this speculation by a group of scientists that the way in which some people talk or breathe might spread many more potential coronavirus-carrying droplets than other people.

The scientists also have found intriguing evidence that a small subset of people may behave as “speech superemitters” — individuals who consistently broadcast an order of magnitude more respiratory particles than their peers. “It is very difficult to identify who is going to be a superemitter ahead of time,” he says. “One of the superemitters was a very petite young woman. And I was a bigger, bulkier guy and was not a superemitter.”

I don’t know why I find this so interesting, but I do. Add “speech superemitter” to the list of new Covid-19 vocabulary.

Who Is Responsible For Climate Change?

posted by Jason Kottke   Jun 23, 2020

In their newest video, Kurzgesagt explores the question of responsibility around climate change: which countries are most responsible for carbon emissions and for fixing the damage they’ve caused. As always, their source material is worth a look.

The Pandemic’s Epidemic of Loneliness

posted by Jason Kottke   Jun 22, 2020

In The Price of Isolation for Rolling Stone, Alex Morris writes about how trends toward increasing social isolation in America left us ill-prepared to face weeks and months of time by ourselves during the pandemic. Studies have shown that humans in isolation are less healthy and less able to fight off disease than when other humans are around. This part in particular really really resonated with me:

Sometimes, though, the body can be tricked. When Cole and his colleagues started looking for ways to combat the physical effects of loneliness, they didn’t find that positive emotions made a difference at all. But one thing did: “It was something called eudaimonic well-being, which is a sense of purpose and meaning, a sense of a commitment to some kind of self-transcendent goal greater than your own immediate self-gratification. People who have a lot of connection to some life purpose? Their biology looked great.” Even when researchers compared lonely people with purpose to social butterflies without it, purpose came out on top. In other words, it’s possible when we’re doing things to better our society, the body assumes there’s a society there to better. We’re technically alone, but it doesn’t feel that way.

Which has profound implications in the moment in which we currently find ourselves, a moment when the physical isolation and disconnection the virus has inflicted is now layered over the clear divisions and systemic inequities that have always plagued our country. In the midst of our solitude, we’ve been confronted with the terrible knowledge that people of color are dying of the virus at the highest rates and that 40 percent of families making less than $40,000 a year have lost their livelihoods. We’ve been confronted with the killings of Ahmaud Arbery, Breonna Taylor, and George Floyd. We’ve been confronted with the lie that the virus is a great equalizer. We’ve witnessed the many ways it isn’t.

See also We’re All Lonely Together and An Epidemic of Middle-aged Male Loneliness.

The 1850s Map that Made Modern Epidemiology

posted by Jason Kottke   Jun 18, 2020

In 1854, Dr. John Snow produced a map of a London cholera outbreak which showed deaths from the disease concentrated around a water pump on Broad Street. The prevailing view at the time was that cholera spread through dirty air, but Snow hypothesized that it was actually spread through water and constructed this early medical data visualization to help prove it.

John Snow Cholera Map

Through a mix of personal interviews, clever detective work, and data analysis that included tables and a famous map, Snow managed to stop the outbreak and convince local public health officials, eventually, that cholera could be transmitted through water, not a miasma. Since his breakthrough study, the map has become an iconic piece of epidemiological history, as an illustration of keen detective work, analysis, and visual representation with a map that, even today, tells a story.

Aside from the cluster of deaths around the pump (which could be argued were the result of a miasma cloud and not contaminated water), stories of nearby people who didn’t get sick (brewers who drank the beer they produced rather than well water, people in buildings with their own wells) and far away people who died because they had drunk water from the well were also essential in proving his theory:

I was informed by this lady’s son that she had not been in the neighbourhood of Broad Street for many months. A cart went from broad Street to West End every day and it was the custom to take out a large bottle of the water from the pump in Broad Street, as she preferred it. The water was taken on Thursday 31st August., and she drank of it in the evening, and also on Friday. She was seized with cholera on the evening of the latter day, and died on Saturday

You can read more about John Snow and how his map changed science and medicine in Steven Johnson’s excellent Ghost Map.

A Visual Guide to the SARS-CoV-2 Coronavirus

posted by Jason Kottke   Jun 17, 2020

Inside SARS-CoV-2

For its July 2020 issue, Scientific American has published A Visual Guide to the SARS-CoV-2 Coronavirus detailing what scientists have learned about this tiny menace that’s brought our world to a halt.

In the graphics that follow, Scientific American presents detailed explanations, current as of mid-May, into how SARS-CoV-2 sneaks inside human cells, makes copies of itself and bursts out to infiltrate many more cells, widening infection. We show how the immune system would normally attempt to neutralize virus particles and how CoV-2 can block that effort. We explain some of the virus’s surprising abilities, such as its capacity to proofread new virus copies as they are being made to prevent mutations that could destroy them. And we show how drugs and vaccines might still be able to overcome the intruders.

Vietnam, Population 95 Million, Has Recorded 0 Deaths from Covid-19

posted by Jason Kottke   Jun 16, 2020

Several countries have been celebrated for their success in curtailing the Covid-19 pandemic — Iceland, New Zealand, Mongolia, Hong Kong, Taiwan — but Vietnam, a nation of 95 million people that borders China, has recorded only 334 total infections and 0 deaths. 0 deaths. They are currently on a 61-day streak without a single community transmission. (For reference, the US has recorded 2.1 million cases and more than 115,000 deaths with just 3.4 times the population of Vietnam.)

How have they done it? They acted early and aggressively.

Experts say experience dealing with prior pandemics, early implementation of aggressive social distancing policies, strong action from political leaders and the muscle of a one-party authoritarian state have helped Vietnam.

“They had political commitment early on at the highest level,” says John MacArthur, the U.S. Centers for Disease Control and Prevention’s country representative in neighboring Thailand. “And that political commitment went from central level all the way down to the hamlet level.”

With experience gained from dealing with the 2003 SARS and 2009 H1N1 pandemics, Vietnam’s government started organizing its response in January — as soon as reports began trickling in from Wuhan, China, where the virus is believed to have originated. The country quickly came up with a variety of tactics, including widespread quarantining and aggressive contact tracing. It has also won praise from the World Health Organization and the CDC for its transparency in dealing with the crisis.

From the BBC:

Vietnam enacted measures other countries would take months to move on, bringing in travel restrictions, closely monitoring and eventually closing the border with China and increasing health checks at borders and other vulnerable places.

Schools were closed for the Lunar New Year holiday at the end of January and remained closed until mid-May. A vast and labour intensive contact tracing operation got under way.

“This is a country that has dealt with a lot of outbreaks in the past,” says Prof Thwaites, from Sars in 2003 to avian influenza in 2010 and large outbreaks of measles and dengue.

“The government and population are very, very used to dealing with infectious diseases and are respectful of them, probably far more so than wealthier countries. They know how to respond to these things.”

By mid-March, Vietnam was sending everyone who entered the country - and anyone within the country who’d had contact with a confirmed case — to quarantine centres for 14 days.

Costs were mostly covered by the government, though accommodation was not necessarily luxurious. One woman who flew home from Australia — considering Vietnam a safer place to be - told BBC News Vietnamese that on their first night they had “only one mat, no pillows, no blankets” and one fan for the hot room.

Forced bussing to quarantine centers in the US, could you even imagine? Better that hundreds of thousands of people die, I guess.

The Vietnamese health system also implemented aggressive contact tracing:

Authorities rigorously traced down the contacts of confirmed coronavirus patients and placed them in a mandatory two-week quarantine.

“We have a very strong system: 63 provincial CDCs (centers for disease control), more than 700 district-level CDCs, and more than 11,000 commune health centers. All of them attribute to contact tracing,” said doctor Pham with the National Institute of Hygiene and Epidemiology.

A confirmed coronavirus patient has to give health authorities an exhaustive list of all the people he or she has met in the past 14 days. Announcements are placed in newspapers and aired on television to inform the public of where and when a coronavirus patient has been, calling on people to go to health authorities for testing if they have also been there at the same time, Pham said.

More from Axios and The Guardian.

Jesus Christ, Just Wear a Face Mask!

posted by Jason Kottke   Jun 11, 2020

The conclusion from a recent paper in the Proceedings of the Royal Society A:

We conclude that facemask use by the public, when used in combination with physical distancing or periods of lock-down, may provide an acceptable way of managing the COVID-19 pandemic and re-opening economic activity. These results are relevant to the developed as well as the developing world, where large numbers of people are resource poor, but fabrication of home-made, effective facemasks is possible. A key message from our analyses to aid the widespread adoption of facemasks would be: ‘my mask protects you, your mask protects me’.

From a Reuters report on the paper:

The research, led by scientists at the Britain’s Cambridge and Greenwich Universities, suggests lockdowns alone will not stop the resurgence of the new SARS-CoV-2 coronavirus, but that even homemade masks can dramatically reduce transmission rates if enough people wear them in public.

“Our analyses support the immediate and universal adoption of face masks by the public,” said Richard Stutt, who co-led the study at Cambridge.

A pair of recent papers used the geographic differences in mask usage in Germany to gauge the effectiveness of masks in preventing the spread of Covid-19. Face Masks Considerably Reduce COVID-19 Cases in Germany:

We use the synthetic control method to analyze the effect of face masks on the spread of Covid-19 in Germany. Our identification approach exploits regional variation in the point in time when face masks became compulsory. Depending on the region we analyse, we find that face masks reduced the cumulative number of registered Covid-19 cases between 2.3% and 13% over a period of 10 days after they became compulsory. Assessing the credibility of the various estimates, we conclude that face masks reduce the daily growth rate of reported infections by around 40%.

And Compulsory face mask policies do not affect community mobility in Germany suggests that people don’t go out more or “feel invincible” when they’re wearing masks:

We use anonymised GPS data from Google’s Location History feature to measure daily mobility in public spaces (groceries and pharmacies, transport hubs and workplaces). We find no evidence that compulsory face mask policies affect community mobility in public spaces in Germany. The evidence provided in this paper makes a crucial contribution to ongoing debates about how to best manage the COVID-19 pandemic.

And these are just from the last few days. Why WHY WHY!!!! are we still talking about this? There’s no credible evidence that wearing a mask is harmful, so at worse it’s harmless. If there’s like a 1-in-10 chance that masks are somewhat helpful — and the growing amount of research suggests that both 1-in-10 and “somewhat helpful” are both understatements — isn’t it worth the tiny bit of effort to wear one and help keep our neighbors safe from potential fucking death? Just in case?

I mean, look at where we are as a country right now. Most of the US is reopening while the number of infections continue to rise. Testing is still not where it needs to be in many areas. Tracing and isolation are mostly not happening. According to epidemiologists, those are the minimum things you need to do to properly contain a pandemic like this. Maybe if you’re Iceland you can pooh pooh the efficacy of masks because you test/trace/isolated to near-perfection, but if you’re going to half-ass it like the US has chosen to do, then wearing masks under semi-lockdown conditions is all we have left! Can we do the bare minimum that is asked of us?

Update: And some anecdotal evidence from Missouri: two hairstylists saw 140 clients while symptomatic last month and it resulted in zero infections. Both the hairstylists and their clients wore masks and took other precautions (staggered appointments, chairs spaced apart).

Update: I deleted a reference to this paper that many epidemiologists et al. have flagged as problematic (see here, here, and here for instance). (via @harrislapiroff)

The Masks Masquerade by Nassim Nicholas Taleb is worth a read.

“Libertarians” (in brackets) are resisting mask wearing on grounds that it constrains their freedom. Yet the entire concept of liberty lies in the Non-Aggression Principle, the equivalent of the Silver Rule: do not harm others; they in turn should not harm you. Even more insulting is the demand by pseudolibertarians that Costco should banned from forcing customers to wear mask — but libertarianism allows you to set the rules on your own property. Costco should be able to force visitors to wear pink shirts and purple glasses if they wished.

Note that by infecting another person you are not infecting just another person. You are infecting many many more and causing systemic risk.

Wear a mask. For the Sake of Others.

And finally, obviously, if wearing a mask is not advisable for you — for a genuine medical reason or if it makes you look dangerous to a racist policing system for instance — then you shouldn’t wear one! But the vast majority of us should be able to manage it.

Update: A study in Health Affairs analyzing the infection rates in US states with face mask mandates versus those without finds that a mandate was associated with a decline in the Covid-19 growth rate (italics mine).

Mandating face mask use in public is associated with a decline in the daily COVID-19 growth rate by 0.9, 1.1, 1.4, 1.7, and 2.0 percentage points in 1-5, 6-10, 11-15, 16-20, and 21+ days after signing, respectively. Estimates suggest as many as 230,000-450,000 COVID-19 cases possibly averted By May 22, 2020 by these mandates. The findings suggest that requiring face mask use in public might help in mitigating COVID-19 spread.

In a comparison among countries, those where people wore masks early fared much better than those where people didn’t. This is a pretty stark difference:

Mask vs. non-mask mortality

And this study noted that Google search volume of people searching for masks in various countries correlated with the infection rate — in general, the earlier the search volume increased in a given country, the fewer infections recorded in that country.

For Some, the Effects of Covid-19 Last for Months

posted by Jason Kottke   Jun 04, 2020

The Atlantic’s Ed Yong interviewed several people who, like thousands of others around the world, have been experiencing symptoms of Covid-19 for months now, indicating that the disease is chronic for some. Thousands Who Got COVID-19 in March Are Still Sick:

I interviewed nine of them for this story, all of whom share commonalities. Most have never been admitted to an ICU or gone on a ventilator, so their cases technically count as “mild.” But their lives have nonetheless been flattened by relentless and rolling waves of symptoms that make it hard to concentrate, exercise, or perform simple physical tasks. Most are young. Most were previously fit and healthy. “It is mild relative to dying in a hospital, but this virus has ruined my life,” LeClerc said. “Even reading a book is challenging and exhausting. What small joys other people are experiencing in lockdown-yoga, bread baking-are beyond the realms of possibility for me.”

One of those who has been sick for months is Paul Garner, a professor of infectious diseases:

It “has been like nothing else on Earth,” said Paul Garner, who has previously endured dengue fever and malaria, and is currently on day 77 of COVID-19. Garner, an infectious-diseases professor at the Liverpool School of Tropical Medicine, leads a renowned organization that reviews scientific evidence on preventing and treating infections. He tested negative on day 63. He had waited to get a COVID-19 test partly to preserve them for health-care workers, and partly because, at one point, he thought he was going to die. “I knew I had the disease; it couldn’t have been anything else,” he told me. I asked him why he thought his symptoms had persisted. “I honestly don’t know,” he said. “I don’t understand what’s happening in my body.”

Garner wrote about his experience for BMJ.

The illness went on and on. The symptoms changed, it was like an advent calendar, every day there was a surprise, something new. A muggy head; acutely painful calf; upset stomach; tinnitus; pins and needles; aching all over; breathlessness; dizziness; arthritis in my hands; weird sensation in the skin with synthetic materials. Gentle exercise or walking made me worse — I would feel absolutely dreadful the next day. I started talking to others. I found a marathon runner who had tried 8 km in her second week, which caused her to collapse with rigors and sleep for 24 hours. I spoke to others experiencing weird symptoms, which were often discounted by those around them as anxiety, making them doubt themselves.

We still have no idea what the long-term effects of this disease are going to be. But it is definitely not the flu. And I remain unwilling to risk myself or my family getting it.

How to Read a Scientific Paper

posted by Jason Kottke   Jun 03, 2020

With the Covid-19 pandemic and the reams of research scientists are producing in trying to understand it, many people are reading scientific research papers for the first time. Long-time science writer Carl Zimmer, who estimates he’s read tens of thousands of them in his career, provides some useful guidance in how to read them.

When you read through a scientific paper, it’s important to maintain a healthy skepticism. The ongoing flood of papers that have yet to be peer-reviewed — known as preprints — includes a lot of weak research and misleading claims. Some are withdrawn by the authors. Many will never make it into a journal. But some of them are earning sensational headlines before burning out in obscurity.

In April, for example, a team of Stanford researchers published a preprint in which they asserted that the fatality rate of Covid-19 was far lower than other experts estimated. When Andrew Gelman, a Columbia University statistician, read their preprint, he was so angry he publicly demanded an apology.

“We wasted time and effort discussing this paper whose main selling point was some numbers that were essentially the product of a statistical error,” he wrote on his blog.

Developing research-reading skills can also be helpful for activists attempting to drive change using data about policing & racism in America. (Just be aware that recent scientific studies have shown the limitations of facts in changing human minds.)

Research on How to Stop Police Violence

posted by Jason Kottke   Jun 01, 2020

From Samuel Sinyangwe, a thread about research-based solutions to stop police violence. Body cams & police training programs don’t reduce police violence, but demilitarization, stricter use-of-force policies, and better police union contracts do (among other things).

More restrictive state and local policies governing police use of force are associated with significantly lower rates of police shootings/killings by police. This is backed by 30+ years of research.

Demilitarization. Police depts that get more military weapons from the federal govt kill more people. You can stop that from happening through local and state policy. Montana (Red state) has gone the furthest on this.

Police Union Contracts. Every 4-6 years your police dept’s accountability system is re-negotiated. Purging misconduct records, reinstating fired officers, dept funding- it’s in the contract. Cities with worse contracts have higher police violence rates.

You can learn more about this research at Campaign Zero.

The Country with the Best Covid-19 Response? Mongolia.

posted by Jason Kottke   May 26, 2020

Mongolia Covid-19 response

Several countries have had solid responses to the Covid-19 pandemic: Taiwan, South Korea, New Zealand, and Hong Kong. But Indi Samarajiva thinks we should be paying much more attention to Mongolia, a country of 3.17 million people where no one has died and no locally transmitted cases have been reported.1 Let’s have that again: 3.17 million people, 0 local cases, 0 deaths. How did they do it? They saw what was happening in Wuhan, coordinated with the WHO, and acted swiftly & decisively in January.

Imagine that you could go back in time to January 23rd with the horse race results and, I dunno, the new iPhone. People believe you. China has just shut down Hubei Province, the largest cordon sanitaire in human history. What would you scream to your leaders? What would you tell them to do?

You’d tell them that this was serious and that it’s coming for sure. You’d tell them to restrict the borders now, to socially distance now, and to get medical supplies ready, also now. You’d tell them to react right now, in January itself. That’s 20/20 hindsight.

That’s exactly what Mongolia did, and they don’t have a time machine. They just saw what was happening in Hubei, they coordinated with China and the WHO, and they got their shit together fast. That’s their secret, not the elevation. They just weren’t dumb.

When you go to World In Data’s Coronavirus Data Explorer and click on “Mongolia” to add their data to the graph, nothing happens because they have zero reported cases and zero deaths. They looked at the paradox of preparation — the idea that “when the best way to save lives is to prevent a disease rather than treat it, success often looks like an overreaction” — and said “sign us up for the overreacting!”

Throughout February, Mongolia was furiously getting ready - procuring face masks, test kits, and PPE; examining hospitals, food markets, and cleaning up the city. Still no reported cases. Still no let-up in readiness. No one was like “it’s not real!” or “burn the 5G towers!”

The country also suspended their New Year celebrations, which are a big deal in Asia. They deployed hundreds of people and restricted intercity travel to make sure, though the public seemed to broadly support the move.

Again — and I’ll keep saying this until March — there were still NO CASES. If you want to know how Mongolia ended up with no local cases, it’s because they reacted when there were no local cases. And they kept acting.

For example, when they heard of a case across the border (ie, not in Mongolia) South Gobi declared an emergency and put everyone in masks. The center also shut down coal exports — a huge economic hit, which they took proactively.

As you can see, at every turn they’re reacting like other countries only did when it was too late. This looked like an over-reaction, but in fact, Mongolia was always on time.

I have to tell you true: I got really upset reading this. Like crying and furious. The United States could have done this. Italy could have done this. Brazil could have done this. Sweden could have done this. England could have done this. Spain could have done this. Mongolia listened to the experts, acted quickly, and kept their people safe. Much of the rest of the world, especially the western world — the so-called first-world countries — failed to act quickly enough and hundreds of thousands of people have needlessly died and countless others have been left with chronic health issues, grief, and economic chaos.

  1. If you look at the list of cases at the bottom of this article (translated by Google), you can see that every reported case is from people coming into the country who were tested and quarantined.

Just When You Thought It Was Safe to Go Back Into the Water…

posted by Jason Kottke   May 21, 2020

As summer ramps up in North America, people are looking to get out to enjoy the weather while also trying to keep safe from Covid-19 infection. Here in Vermont, I am very much looking forward to swim hole season and have been wondering if swimming is a safe activity during the pandemic. The Atlantic’s Olga Khazan wrote about the difficulty of opening pools back up this summer:

The coronavirus can’t remain infectious in pool water, multiple experts assured me, but people who come to pools do not stay in the water the entire time. They get out, sit under the sun, and, if they’re like my neighbors, form a circle and drink a few illicit White Claws. Social-distancing guidelines are quickly forgotten.

“If someone is swimming laps, that would be pretty safe as long as they’re not spitting water everywhere,” says Angela Rasmussen, a virologist at Columbia University. “But a Las Vegas-type pool party, that would be less safe, because people are just hanging out and breathing on each other.”

This story by Christopher Reynolds in the LA Times focuses more on transmission via water (pool water, salt water, river/lake water).

“There is no data that somebody got infected this way [with coronavirus],” said professor Karin B. Michels, chair of UCLA’s Department of Epidemiology, in a recent interview.

“I can’t say it’s absolutely 100% zero risk, but I can tell you that it would never cross my mind to get COVID-19 from a swimming pool or the ocean,” said Paula Cannon, a professor of molecular microbiology and immunology at USC’s Keck School of Medicine. “It’s just extraordinarily unlikely that this would happen.”

As long as you keep your distance of course:

Rather than worry about coronavirus in water, UCLA’s Michels and USC’s Cannon said, swimmers should stay well separated and take care before and after entering the pool, lake, river or sea.

“I would be more concerned about touching the same lockers or surfaces in the changing room or on the benches outside the pool. Those are higher risk than the water itself,” Michels said. “The other thing is you have to maintain distance. … More distance is always better.”

Sorta related but not really: ten meters is definitely more distance.

Flat Earthers Listening to Daft Punk

posted by Jason Kottke   May 12, 2020

This made me laugh really hard today:

Gotta be frustrating. ♪ Around the world, around the world, around the world, around the world, around the world, around the world… ♪ (thx, naomi)

A Practical Guide to Covid-19 Risks and How to Avoid Them

posted by Jason Kottke   May 11, 2020

As some places in the United States and other countries are opening back up (some very prematurely), immunologist and biologist Dr. Erin Bromage has written a practical guide to the known Covid-19 risks and how to avoid them that’s based on recent scientific research. He begins:

It seems many people are breathing some relief, and I’m not sure why. An epidemic curve has a relatively predictable upslope and once the peak is reached, the back slope can also be predicted. We have robust data from the outbreaks in China and Italy, that shows the backside of the mortality curve declines slowly, with deaths persisting for months. Assuming we have just crested in deaths at 70k, it is possible that we lose another 70,000 people over the next 6 weeks as we come off that peak. That’s what’s going to happen with a lockdown.

As states reopen, and we give the virus more fuel, all bets are off. I understand the reasons for reopening the economy, but I’ve said before, if you don’t solve the biology, the economy won’t recover.

But since things are opening up anyway (whether epidemiologists like it or not), Bromage goes through a number of scenarios you might potentially find yourself in over the next few months and what the associated risks might be. His guiding principle is that infection is caused by exposure to the virus over time — increase the time or the exposure and your risk goes up. For example, public bathrooms might give you a ton of exposure to the virus over a relatively short period of time:

Bathrooms have a lot of high touch surfaces, door handles, faucets, stall doors. So fomite transfer risk in this environment can be high. We still do not know whether a person releases infectious material in feces or just fragmented virus, but we do know that toilet flushing does aerosolize many droplets. Treat public bathrooms with extra caution (surface and air), until we know more about the risk.

But being in the same room with another person simply breathing may not carry a large risk if you limit the time.

A single breath releases 50-5000 droplets. Most of these droplets are low velocity and fall to the ground quickly. There are even fewer droplets released through nose-breathing. Importantly, due to the lack of exhalation force with a breath, viral particles from the lower respiratory areas are not expelled.

But that time would drop sharply if the person is speaking:

Speaking increases the release of respiratory droplets about 10 fold; ~200 copies of virus per minute. Again, assuming every virus is inhaled, it would take ~5 minutes of speaking face-to-face to receive the required dose.

Again, this is all indoors. Being in enclosed spaces with other humans, particularly if they are poorly ventilated, is going to hold higher risks for the foreseeable future.

The reason to highlight these different outbreaks is to show you the commonality of outbreaks of COVID-19. All these infection events were indoors, with people closely-spaced, with lots of talking, singing, or yelling. The main sources for infection are home, workplace, public transport, social gatherings, and restaurants. This accounts for 90% of all transmission events. In contrast, outbreaks spread from shopping appear to be responsible for a small percentage of traced infections. (Ref)

Importantly, of the countries performing contact tracing properly, only a single outbreak has been reported from an outdoor environment (less than 0.3% of traced infections). (ref)

The Michael Pollan version of advice for socializing during the pandemic might be: Spend time with people, not too much, mostly masked and outdoors.

On the Accuracy of Covid-19 Testing

posted by Jason Kottke   May 07, 2020

As someone who suspects I may have had a mild case of Covid-19 a couple of months ago, I’ve been thinking about getting tested for antibodies. But as this video from ProPublica shows, even really accurate tests may not actually tell you all that much.

And the thing is, the “do I have Covid-19 right now” tests are plagued by the same issue.

For patients getting tested, the main concern is how to interpret the outcome: If I test negative with an RT-PCR genetic test, what are the chances I actually have the virus? Or if I test positive with an antibody test, does it actually mean I have the antibodies?

It turns out that the answers to these questions don’t just hinge on the accuracy of the test. “Mathematically, the way that works out, that actually depends on how many people in your area have Covid,” Eleanor Murray, an assistant professor of epidemiology at the Boston University School of Public Health, said.

The rarer the disease in the population, the less you’ll learn by testing.

Let’s say we have a hypothetical Covid-19 test for antibodies that is both 99 percent sensitive — meaning almost all people with antibodies will test positive — and 99 percent specific, meaning almost all people who were never infected will yield a negative result.

If you test a group of 100 uninfected people, odds are one of them will still test positive even though they don’t have the virus. Conversely, if you test 100 people who were infected, it’s likely one of them will still test negative.

Now let’s presume the virus has a prevalence rate of 1 percent, so one person in 100 carries antibodies to it. If you test 100 random people and get a positive result, what is the chance that this person was truly infected?

Deborah Birx, the White House Covid-19 response coordinator, explained the answer at a press conference on April 20: “So if you have 1 percent of your population infected and you have a test that’s only 99 percent specific, that means that when you find a positive, 50 percent of the time will be a real positive and 50 percent of the time it won’t be.”

So even if I test positive for antibodies and I assume that confers immunity, given that the number of confirmed infections in Vermont is so low (~900 statewide), it doesn’t seem like I would be justified in changing my behavior at all. I would still have to act as though I’ve never had the virus, both for my own health and the health of those around me. Maybe if I had two or three corroborating tests could I be more certain…

SARS-CoV-2, An Emerging Portrait

posted by Jason Kottke   May 06, 2020

From Nature’s David Cyranoski, a piece that takes a look at what the latest research says about SARS-CoV-2, where it came from, and how it is able to infect the human body. I’m going to highlight a few things from the article I thought were particularly interesting. As Cyranoski has done throughout, I’d like to stress that because this virus is so new to us and the situation is moving so quickly, many of these results are based on preliminary research, have been published in pre-print papers, and haven’t been peer-reviewed.

The first is about the detective work being done to trace where SARS-CoV-2 came from and how long it’s been in existence (possibly decades).

SARS-CoV-2 genetic origin

But studies released over the past few months, which have yet to be peer-reviewed, suggest that SARS-CoV-2 — or a very similar ancestor — has been hiding in some animal for decades. According to a paper posted online in March, the coronavirus lineage leading to SARS-CoV-2 split more than 140 years ago from the closely related one seen today in pangolins. Then, sometime in the past 40-70 years, the ancestors of SARS-CoV-2 separated from the bat version, which subsequently lost the effective receptor binding domain that was present in its ancestors (and remains in SARS-CoV-2). A study published on 21 April came up with very similar findings using a different dating method.

The section on how the virus acts in the body is particularly interesting because it attempts to explain the unusual and varying behaviors SARS-CoV-2 exhibits and causes in different parts of the human body. For example, SARS-CoV-2, unusually, can initially infect two places in the body: the throat and lungs.

Having these two infection points means that SARS-CoV-2 can mix the transmissibility of the common cold coronaviruses with the lethality of MERS-CoV and SARS-CoV. “It is an unfortunate and dangerous combination of this coronavirus strain,” he says.

The virus’s ability to infect and actively reproduce in the upper respiratory tract was something of a surprise, given that its close genetic relative, SARS-CoV, lacks that ability. Last month, Wendtner published results of experiments in which his team was able to culture virus from the throats of nine people with COVID-19, showing that the virus is actively reproducing and infectious there. That explains a crucial difference between the close relatives. SARS-CoV-2 can shed viral particles from the throat into saliva even before symptoms start, and these can then pass easily from person to person. SARS-CoV was much less effective at making that jump, passing only when symptoms were full-blown, making it easier to contain.

These differences have led to some confusion about the lethality of SARS-CoV-2. Some experts and media reports describe it as less deadly than SARS-CoV because it kills about 1% of the people it infects, whereas SARS-CoV killed at roughly ten times that rate. But Perlman says that’s the wrong way to look at it. SARS-CoV-2 is much better at infecting people, but many of the infections don’t progress to the lungs. “Once it gets down in the lungs, it’s probably just as deadly,” he says.

And this is a somewhat hopeful speculation on one of the many possible ways the Covid-19 pandemic could go:

“By far the most likely scenario is that the virus will continue to spread and infect most of the world population in a relatively short period of time,” says Stöhr, meaning one to two years. “Afterwards, the virus will continue to spread in the human population, likely forever.” Like the four generally mild human coronaviruses, SARS-CoV-2 would then circulate constantly and cause mainly mild upper respiratory tract infections, says Stöhr. For that reason, he adds, vaccines won’t be necessary.

Some previous studies support this argument. One showed that when people were inoculated with the common-cold coronavirus 229E, their antibody levels peaked two weeks later and were only slightly raised after a year. That did not prevent infections a year later, but subsequent infections led to few, if any, symptoms and a shorter period of viral shedding.

The OC43 coronavirus offers a model for where this pandemic might go. That virus also gives humans common colds, but genetic research from the University of Leuven in Belgium suggests that OC43 might have been a killer in the past.

But then, from a few paragraphs down:

People like to think that “the other coronaviruses were terrible and became mild”, says Perlman. “That’s an optimistic way to think about what’s going on now, but we don’t have evidence.”

For now, it’s just another thing we don’t know about this virus we learned about only 5 months ago. It’s a long road ahead, but I’m thankful that so many scientists are bent on making sense of it all.

What Happens Next? Our Possible Covid-19 Futures…

posted by Jason Kottke   May 04, 2020

Creative technologist Nicky Case and epidemiologist Marcel Salathé have teamed up to produce a concise but thorough playable explainer about important epidemiological concepts, how we could/should respond to the Covid-19 pandemic, and different scenarios about what the next few years could look like.

A gameplan to get R below 1 for coronavirus

If you’ve been keeping up with the various models and experts’ plans (test/trace/isolate, etc.), there’s not a lot new here until close to end, but it is pretty comprehensive and the playable simulations are really useful. The whole thing takes about 30 minutes to get through, but at the end, you will have an excellent simplified understanding of what this virus could do to us and what we can do to mitigate its effects.

Isolating symptomatic cases would reduce R by up to 40%, and quarantining their pre/a-symptomatic contacts would reduce R by up to 50%:

Thus, even without 100% contact quarantining, we can get R < 1 without a lockdown! Much better for our mental & financial health. (As for the cost to folks who have to self-isolate/quarantine, governments should support them — pay for the tests, job protection, subsidized paid leave, etc. Still way cheaper than intermittent lockdown.)

The problem with this explainer, as excellent as it is, is the problem with all of these plans: many government officials on both the state & federal level don’t seem interested in listening to the experts. It is also unclear — if the unmasked crowds gathering in American cities during this past weekend’s warm weather are any indication — that Americans will be willing to take the steps necessary to keep each other safe. I’m not sure what it’s going to take to address those situations, but I don’t think playable graphs are going to help that much.

The Changing Profile of Covid-19’s Presenting Symptoms

posted by Jason Kottke   Apr 29, 2020

As Ed Yong notes in his helpful overview of the pandemic, this is such a huge and quickly moving event that it’s difficult to know what’s happening. Lately, I’ve been seeking information on Covid-19’s presenting symptoms after seeing a bunch of anecdotal data from various sources.

In the early days of the epidemic (January, February, and into March), people were told by the CDC and other public health officials to watch out for three specific symptoms: fever, a dry cough, and shortness of breath. In many areas, testing was restricted to people who exhibited only those symptoms. Slowly, as more data is gathered, the profile of the presenting symptoms has started to shift. From a New York magazine piece by David Wallace-Wells on Monday:

While the CDC does list fever as the top symptom of COVID-19, so confidently that for weeks patients were turned away from testing sites if they didn’t have an elevated temperature, according to the Journal of the American Medical Association, as many as 70 percent of patients sick enough to be admitted to New York State’s largest hospital system did not have a fever.

Over the past few months, Boston’s Brigham and Women’s Hospital has been compiling and revising, in real time, treatment guidelines for COVID-19 which have become a trusted clearinghouse of best-practices information for doctors throughout the country. According to those guidelines, as few as 44 percent of coronavirus patients presented with a fever (though, in their meta-analysis, the uncertainty is quite high, with a range of 44 to 94 percent). Cough is more common, according to Brigham and Women’s, with between 68 percent and 83 percent of patients presenting with some cough — though that means as many as three in ten sick enough to be hospitalized won’t be coughing. As for shortness of breath, the Brigham and Women’s estimate runs as low as 11 percent. The high end is only 40 percent, which would still mean that more patients hospitalized for COVID-19 do not have shortness of breath than do. At the low end of that range, shortness of breath would be roughly as common among COVID-19 patients as confusion (9 percent), headache (8 to 14 percent), and nausea and diarrhea (3 to 17 percent).

Recently, as noted by the Washington Post, the CDC has changed their list of Covid-19 symptoms to watch out for. They now list two main symptoms (cough & shortness of breath) and several additional symptoms (fever, chills, repeated shaking with chills, muscle pain, headache, sore throat, new loss of taste or smell). They also note that “this list is not all inclusive”. Compare that with their list from mid-February.

In addition, there’s evidence that children might have different symptoms (including stomach issues or diarrhea), doctors are reporting seeing “COVID toes” on some patients, and you might want to look at earlier data from these three studies about symptoms observed in Wuhan and greater China.

The reason I’m interested in this shift in presenting symptoms is that on the last day or two of my trip to Asia, I got sick — and I’m been wondering if it was Covid-19.

Here’s the timeline: starting on Jan 21, I was in Saigon, Vietnam for two weeks, then in Singapore for 4 days, and then Doha, Qatar for 48 hours. The day I landed in Doha, Feb 9, I started to feel a little off, and definitely felt sick the next day. I had a sore throat, headache, and congestion (stuffy nose) for the first few days. There was also some fatigue/tiredness but I was jetlagged too so… All the symptoms were mild and it felt like a normal cold to me. Here’s how I wrote about it in my travelogue:

I got sick on the last day of the trip, which turned into a full-blown cold when I got home. I dutifully wore my mask on the plane and in telling friends & family about how I was feeling, I felt obliged to text “***NOT*** coronavirus, completely different symptoms!!”

I flew back to the US on Feb 11 (I wore a mask the entire time in the Doha airport, on the plane, and even in the Boston airport, which no one else was doing). I lost my sense of taste and smell for about 2 days, which was a little unnerving but has happened to me with past colds. At no point did I have even the tiniest bit of fever or shortness of breath. The illness did drag on though — I felt run-down for a few weeks and a very slight cough that developed about a week and a half after I got sick lingered for weeks.

According to guidance from the WHO, CDC, and public health officials at the time, none of my initial symptoms were a match for Covid-19. I thought about getting a test or going to the doctor, but in the US in mid-February, and especially in Vermont, there were no tests available for someone with a mild cold and no fever. But looking at the CDC’s current list of symptoms — which include headache, sore throat, and new loss of taste or smell — and considering that I’d been in Vietnam and Singapore when cases were reported in both places, it seems plausible to me that my illness could have been a mild case of Covid-19. Hopefully it wasn’t, but I’ll be getting an antibody test once they are (hopefully) more widely available, even though the results won’t be super reliable.

Update: More on the changing profile of Covid-19 symptoms from a sample size of more than 30,000 tests.

Covid-19 presenting symptoms

Fever is waaay down on the list.

While not as common as other symptoms, loss of smell was the most highly correlated with testing positive, as shown with odds ratios below, after adjusting for age and gender. Those with loss of smell were more likely to test positive for COVID-19 than those with a high fever.

Seeing this makes me think more than ever that I had it. I had three of the top five symptoms, plus an eventual cough (the most common symptom) and a loss of smell & taste (the most highly correlated symptom). The timing of the onset of my symptoms (my first day in Qatar) indicates that I probably got infected on my last day in Vietnam, in transit from Vietnam to Singapore (1 2-hr plane ride, 2 airports, 1 taxi, 1 train ride), or on my first day in Singapore. But I went to so many busy places during that time that it’s impossible to know where I might have gotten infected (or who I then went on to unwittingly infect).

How We Reopen the Country: A Roadmap to Pandemic Resilience

posted by Jason Kottke   Apr 20, 2020

Working under the direction of The Edmond J. Safra Center for Ethics at Harvard University, a bipartisan group of experts in public health, economics, technology, and ethics have produced a plan for a phased reopening of public life in the United States through testing, tracing, and supported isolation. The video above summarizes the plan and here’s the full plan in the form of a 56-page PDF.

“Roadmap to Pandemic Resilience: Massive Scale Testing, Tracing, and Supported Isolation (TTSI) as the Path to Pandemic Resilience for a Free Society,” lays out how a massive scale-up of testing, paired with contact tracing and supported isolation, can rebuild trust in our personal safety and re-mobilize the U.S. economy.

Among the report’s top recommendations is the need to deliver at least 5 million tests per day by early June to help ensure a safe social opening. This number will need to increase to 20 million tests per day by mid-summer to fully re-mobilize the economy.

Pandemic Resilience

From the paper, here’s a quick overview:

What we need to do is much bigger than most people realize. We need to massively scale-up testing, contact tracing, isolation, and quarantine-together with providing the resources to make these possible for all individuals.

Broad and rapid access to testing is vital for disease monitoring, rapid public health response, and disease control.

We need to deliver 5 million tests per day by early June to deliver a safe social reopening. This number will need to increase over time (ideally by late July) to 20 million a day to fully remobilize the economy. We acknowledge that even this number may not be high enough to protect public health. In that considerably less likely eventuality, we will need to scale-up testing much further. By the time we know if we need to do that, we should be in a better position to know how to do it. In any situation, achieving these numbers depends on testing innovation.

Between now and August, we should phase in economic mobilization in sync with growth in our capacity to provide sustainable testing programs for mobilized sectors of the workforce.

The great value of this approach is that it will prevent cycles of opening up and shutting down. It allows us to steadily reopen the parts of the economy that have been shut down, protect our frontline workers, and contain the virus to levels where it can be effectively managed and treated until we can find a vaccine.

We can have bottom-up innovation and participation and top-down direction and protection at the same time; that is what our federal system is designed for.

This policy roadmap lays out how massive testing plus contact tracing plus social isolation with strong social supports, or TTSI, can rebuild trust in our personal safety and the safety of those we love. This will in turn support a renewal of mobility and mobilization of the economy. This paper is designed to educate the American public about what is emerging as a consensus national strategy.

The plan seems consistent with what economist Paul Romer has been saying — Without More Tests, America Can’t Reopen (And to make matters worse, we’re testing the wrong people) — and with the approach Hong Kong has been taking — Test and trace: lessons from Hong Kong on avoiding a coronavirus lockdown. See also the 4 plans to end social distancing, explained.

Unfortunately for this plan and for all of us, I have a feeling that the first true step in any rational plan to reopen the United States without unnecessary death and/or massive economic disruption that lasts for years is the removal of Donald Trump from office (and possibly also the end of the Republican-controlled Senate). Barring that, the ineffectual circus continues. (via @riondotnu)

The Emerging Science of What SARS-CoV-2 Does to the Human Body

posted by Jason Kottke   Apr 20, 2020

Thousands of scientific research papers on Covid-19 and SARS-CoV-2 are being published each week and with them comes a clearer picture of the virus and the disease it causes. There’s still a lot we don’t know, but this piece from Science magazine is the best synthesis of the emerging science that I have read. It details a virus that “acts like no microbe humanity has ever seen” and affects not only the lungs but also the kidneys, heart, brain, and the intestines.

As the number of confirmed cases of COVID-19 surges past 2.2 million globally and deaths surpass 150,000, clinicians and pathologists are struggling to understand the damage wrought by the coronavirus as it tears through the body. They are realizing that although the lungs are ground zero, its reach can extend to many organs including the heart and blood vessels, kidneys, gut, and brain.

“[The disease] can attack almost anything in the body with devastating consequences,” says cardiologist Harlan Krumholz of Yale University and Yale-New Haven Hospital, who is leading multiple efforts to gather clinical data on COVID-19. “Its ferocity is breathtaking and humbling.”

Understanding the rampage could help the doctors on the front lines treat the fraction of infected people who become desperately and sometimes mysteriously ill. Does a dangerous, newly observed tendency to blood clotting transform some mild cases into life-threatening emergencies? Is an overzealous immune response behind the worst cases, suggesting treatment with immune-suppressing drugs could help? What explains the startlingly low blood oxygen that some physicians are reporting in patients who nonetheless are not gasping for breath? “Taking a systems approach may be beneficial as we start thinking about therapies,” says Nilam Mangalmurti, a pulmonary intensivist at the Hospital of the University of Pennsylvania (HUP).

How Covid-19 attacks the human body

I’ve been hearing that although Covid-19’s attack begins in the lungs, it is as much a vascular disease as it is a respiratory disease — and there is some evidence emerging to support this view:

If COVID-19 targets blood vessels, that could also help explain why patients with pre-existing damage to those vessels, for example from diabetes and high blood pressure, face higher risk of serious disease. Recent Centers for Disease Control and Prevention (CDC) data on hospitalized patients in 14 U.S. states found that about one-third had chronic lung disease-but nearly as many had diabetes, and fully half had pre-existing high blood pressure.

Mangalmurti says she has been “shocked by the fact that we don’t have a huge number of asthmatics” or patients with other respiratory diseases in HUP’s ICU. “It’s very striking to us that risk factors seem to be vascular: diabetes, obesity, age, hypertension.”

What struck me most about this piece is the sheer energy of the vast network of minds bent towards understanding this thing with the hope of beating it as soon as possible. This is the scientific method at work right here, in all its urgent & messy glory.

Super-Pandemics Last All Summer Long

posted by Jason Kottke   Apr 15, 2020

The Atlantic’s Ed Yong has written his second long article about the Covid-19 pandemic about what happens next and what a roadmap to dealing with the next phase of the crisis might look like.

As I wrote last month, the only viable endgame is to play whack-a-mole with the coronavirus, suppressing it until a vaccine can be produced. With luck, that will take 18 to 24 months. During that time, new outbreaks will probably arise. Much about that period is unclear, but the dozens of experts whom I have interviewed agree that life as most people knew it cannot fully return. “I think people haven’t understood that this isn’t about the next couple of weeks,” said Michael Osterholm, an infectious-disease epidemiologist at the University of Minnesota. “This is about the next two years.”

The pandemic is not a hurricane or a wildfire. It is not comparable to Pearl Harbor or 9/11. Such disasters are confined in time and space. The SARS-CoV-2 virus will linger through the year and across the world. “Everyone wants to know when this will end,” said Devi Sridhar, a public-health expert at the University of Edinburgh. “That’s not the right question. The right question is: How do we continue?”

How Privacy-Friendly Contact Tracing Can Help Stop the Spread of Covid-19

posted by Jason Kottke   Apr 10, 2020

Nicky Case, working with security & privacy researcher Carmela Troncoso and epidemiologist Marcel Salathé, came up with this fantastic explanation of how we can use apps to automatically do contact tracing for Covid-19 infections while protecting people’s privacy. The second panel succinctly explains why contact tracing (in conjunction with quick, ubiquitous testing) can have such a huge benefit in a case like this:

A problem with COVID-19: You’re contagious ~2 days before you know you’re infected. But it takes ~3 days to become contagious, so if we quarantine folks exposed to you the day you know you were infected… We stop the spread, by staying one step ahead!

Contact Tracing Comic

It’s based on a proposal called Decentralized Privacy-Preserving Proximity Tracing developed by Troncoso, Salathé, and a host of others. Thanks to Case for putting this comic in the public domain so that anyone can publish it.

Update: About two hours after posting this, Apple and Google announced they are jointly working on contact tracing technology that uses Bluetooth and makes “user privacy and security central to the design”.

A number of leading public health authorities, universities, and NGOs around the world have been doing important work to develop opt-in contact tracing technology. To further this cause, Apple and Google will be launching a comprehensive solution that includes application programming interfaces (APIs) and operating system-level technology to assist in enabling contact tracing. Given the urgent need, the plan is to implement this solution in two steps while maintaining strong protections around user privacy.

Update: Based on information published by Google and Apple on their contact tracing protocols, it appears as though their system works pretty much like the one outlined about in the comic and this proposal.

Also, here is an important reminder that the problem of what to do about Covid-19 is not primarily a technological one and that turning it into one is troublesome.

We think it is necessary and overdue to rethink the way technology gets designed and implemented, because contact tracing apps, if implemented, will be scripting the way we will live our lives and not just for a short period. They will be laying out normative conditions for reality, and will contribute to the decisions of who gets to have freedom of choice and freedom to decide … or not. Contact tracing apps will co-define who gets to live and have a life, and the possibilities for perceiving the world itself.

Update: Security expert Bruce Schneier has some brief thoughts on “anonymous” contact tracing as well as some links to other critiques, including Ross Anderson’s:

But contact tracing in the real world is not quite as many of the academic and industry proposals assume.

First, it isn’t anonymous. Covid-19 is a notifiable disease so a doctor who diagnoses you must inform the public health authorities, and if they have the bandwidth they call you and ask who you’ve been in contact with. They then call your contacts in turn. It’s not about consent or anonymity, so much as being persuasive and having a good bedside manner.

I’m relaxed about doing all this under emergency public-health powers, since this will make it harder for intrusive systems to persist after the pandemic than if they have some privacy theater that can be used to argue that the whizzy new medi-panopticon is legal enough to be kept running.

And I had thoughts similar to Anderson’s about the potential for abuse:

Fifth, although the cryptographers — and now Google and Apple — are discussing more anonymous variants of the Singapore app, that’s not the problem. Anyone who’s worked on abuse will instantly realise that a voluntary app operated by anonymous actors is wide open to trolling. The performance art people will tie a phone to a dog and let it run around the park; the Russians will use the app to run service-denial attacks and spread panic; and little Johnny will self-report symptoms to get the whole school sent home.

The tie-a-phone-to-a-dog thing reminds me a lot of the wagon full of smartphones creating traffic jams. (via @circa1977)

Covid-19 Now the Leading Cause of Death in America

posted by Jason Kottke   Apr 10, 2020

This week, Covid-19 passed heart disease and cancer as the leading cause of death per day in the United States. In this graph made by Dr. Maria Danilychev using data from Worldometer and the CDC, you can see that Covid-19 overtook heart disease sometime on Monday or Tuesday.

If the data in NYC is any indication, the number of nationwide Covid-19 deaths may be undercounted, so this transition probably happened sooner.1 Hopefully through the social distancing and other measures put in place to flatten the curve, the number of daily Covid-19 deaths won’t start beating out all other causes combined before it starts declining.

  1. Several months from now, it will be easier to get a more accurate count of how many people died by looking at the “baseline” rate of death and comparing it with the actual numbers. Unless this sort of recount is politicized, which it will be, and *siiiigh*

Apollo 11’s Post-Lunar Quarantine

posted by Jason Kottke   Apr 09, 2020

I do not know if hearing about other people’s quarantine experiences makes going through one yourself any easier, but the story of how NASA sequestered the returning Apollo 11 astronauts away from the rest of the world for 21 days is interesting for other reasons as well. The worry was that some sort of “moon bug” or “lunar plague” was going to make its way from the Moon to the Earth in the spacecraft or the astronauts’ bodies.

From the moment the Apollo 11 astronauts arrive back on earth from their epochal visit to the moon, they will be treated not as heroes but as bearers of the most virulent, devastating plague the world has ever known.

So NASA quarantined Armstrong, Aldrin, and Collins in a series of specially designed suits and environments until August 10, 1969. At one point, the three of them lived in a modified Airstream trailer in which the air pressure was lower on the inside than outside so if there was a leak, air would rush into the trailer, not out. Armstrong even celebrated a birthday in quarantine.

After Apollo 11, NASA did similar quarantines for 12 and 14 but abandoned them after that because they figured it was safe.

Oh, and if you were curious about the Soyuz launch yesterday that sent three astronauts to the ISS and how they were going to mitigate the chances of sending any SARS-CoV-2 up there, crews on all missions are subject to a mandatory 2 week quarantine before they leave (according to this press release).

“Strong Evidence” That Social Distancing Is Working to Slow the Spread of Covid-19

posted by Jason Kottke   Apr 09, 2020

Social distancing is working

Trevor Bedford, who does research on epidemics and infectious diseases, has compiled a number of papers and data sets with “strong evidence” that social distancing measures have slowed Covid-19 transmission rates around the world.

This report (from the Imperial College team who produced the sobering report that has been the blueprint for pandemic responses around the world) estimates that measures taken in several European countries have lowered their effective reproduction numbers (the R value) to close to 1.

Overall, we estimate that countries have managed to reduce their reproduction number. Our estimates have wide credible intervals and contain 1 for countries that have implemented all interventions considered in our analysis. This means that the reproduction number may be above or below this value. With current interventions remaining in place to at least the end of March, we estimate that interventions across all 11 countries will have averted 59,000 deaths up to 31 March [95% credible interval 21,000-120,000]. Many more deaths will be averted through ensuring that interventions remain in place until transmission drops to low levels. We estimate that, across all 11 countries between 7 and 43 million individuals have been infected with SARS-CoV-2 up to 28th March, representing between 1.88% and 11.43% of the population. The proportion of the population infected to date — the attack rate — is estimated to be highest in Spain followed by Italy and lowest in Germany and Norway, reflecting the relative stages of the epidemics.

And this was published on March 30 — here’s the latest data. The paper goes on to say (italics mine):

We cannot say for certain that the current measures have controlled the epidemic in Europe; however, if current trends continue, there is reason for optimism.

An Institute for Disease Modeling report from March 29 shows a similar reduction in their effective reproduction number in King County, Washington (the 12th most populous county in the US).

The graphs at the top of the post are from the latest data compiled by the Centre for the Mathematical Modelling of Infectious Diseases. Lots of countries looking like they are headed for an effect R value of 1, which would indicate a slowing (rather than growing) epidemic.

Dozens of Science & Engineering Activities for Kids from The James Dyson Foundation

posted by Jason Kottke   Apr 08, 2020

The James Dyson Foundation has designed a set of 44 challenges related to science & engineering specifically for kids (ages 7 & older), which are perfect for these at-home learning times. The challenges include making an air-powered car out of a balloon, strong bridges out of spaghetti, and a cardboard chair strong enough to hold a person:

Here’s the PDF with all 44 challenges. What I like about these projects is that they’re hands-on, you can do them with stuff you already have around the house, and they’re educational in the best way: there’s no “teaching” really…the challenges are designed to appeal to the natural curiosity of kids.

Reading through these, the one that blew my mind was that you can determine the speed of light by melting a chocolate bar in the microwave.

Microwave Chocolate

That’s so cool! (via open culture)

Dazzling Coronavirus Painting by Biologist David Goodsell

posted by Jason Kottke   Apr 08, 2020

Coronavirus painting by biologist David Goodsell

Since the early 90s, biologist David Goodsell (previously) has been creating scientifically accurate paintings of the structures of cells, molecules, and, yes, viruses. In early February, Goodsell completed a painting of a SARS coronavirus (above).

This painting depicts a coronavirus just entering the lungs, surrounded by mucus secreted by respiratory cells, secreted antibodies, and several small immune systems proteins. The virus is enclosed by a membrane that includes the S (spike) protein, which will mediate attachment and entry into cells, M (membrane) protein, which is involved in organization of the nucleoprotein inside, and E (envelope) protein, which is a membrane channel involved in budding of the virus and may be incorporated into the virion during that process. The nucleoprotein inside includes many copies of the N (nucleocapsid) protein bound to the genomic RNA.

In a brief interview with the NY Times, Goodsell explained why he made the image:

“You have to admit, these viruses are so symmetrical that they’re beautiful,” said Mr. Goodsell, an associate professor at Scripps Research Institute in La Jolla. “Are bright colors and pretty stuff the right approach? The jury’s still out. I’m not trying to make these things look dangerous, I want people to understand how they’re built.”

Seeing the infection count rise, Mr. Goodsell said he worried about the health of his aging parents in Los Angeles. But he hopes his painting can quell fears about the novel coronavirus by educating people on the virus’s workings: “I want people to think of viruses as being an entity that we can learn about and fight. They’re not nebulous nothings.”

Goodsell is currently working on a painting featuring the life cycle of a coronavirus and sharing his progress on Twitter. (via @christopherjobs)

Ken Burns Presents The Gene: An Intimate History

posted by Jason Kottke   Apr 08, 2020

From Ken Burns and Dr. Siddhartha Mukherjee, The Gene: An Intimate History, a series about the history of genetics based on Mukherjee’s book of the same name. Here’s a trailer:

The series tells the story of the rapid evolution of genetic science from Gregor Mendel’s groundbreaking experiment in the 19th century to CRISPR, and the hope that newfound powers to alter DNA with pinpoint precision will transform the treatment of some of the world’s most complex and challenging diseases. The series also tackles the daunting ethical challenges that these technologies pose for humankind.

This looks great, especially if this clip about Nancy Wexler’s crusade to find a cure for Huntington’s disease is representative of the whole:

In 1968, Nancy Wexler’s mother was diagnosed with a rare genetic disease - Huntington’s. Facing a 50-50 chance of contracting Huntington’s herself, Wexler — a non-scientist — began an odyssey to find the gene that causes the disease. For three decades, Wexler searched for treatments but chose not to get tested. As time passed, she noticed changes in the way she moved. Finally, in early 2020, Wexler decided to face her fears.

Part 1 of the series is now streaming on PBS with part 2 set to premiere next week.