Tag Archives: pandemic

about 80% protection against Covid-19 reinfection in a Danish study

When scientists are saying “we are not 100% sure” people who have had Covid-19 will have some immunity to reinfection, many smart people I know are hearing “people who have had Covid-19 have no immunity to infection”. Similarly, when scientists say they are not absolutely sure vaccinated people will not spread the virus (although they are quickly changing their tune on this one as they look at the evidence), people are hearing that vaccinated people are spreading the virus. Here is at least one study showing that when people who had a confirmed infection were tested again three months later, protection against reinfection was pretty good but not perfect at about 80%. It appears to have been lower in people over 65 at about 50%.

The CDC and others have also thrown out 3 months as a minimum amount of time they are confident people are protected against reinfection or protected by a vaccine. I think this is just a conservative estimate in the face of limited information, but again the public is hearing “no protection after 3 months”. In this study, they tested again after 6 months and found no decrease in the level of protection (still about 80%).

So my view is that logic suggests being infected would provide at least some protection against reinfection and being able to spread the virus, and the same for vaccination. I say this because this is how other diseases work. And now the data are backing that up. The science and public health policy communication are still pretty bad, and like a toxic spill, bad communication that takes a few hours can take years to clean up on the surface and there will still be puddles of toxic mess for decades whenever you turn over a rock.

What wild animals were at the Wuhan market?

It seems that the efforts to trace Covid-19 back to bats in the Wuhan province are pretty inconclusive. SARS and MERS were both definitively (?) traced back to bats, so people seem to have jumped to this conclusion. “Similar” viruses have been found in bats, but bats have all kinds of things and the family of coronaviruses seems to be extremely common. The WHO team does say it is extremely unlikely that any of the “several” laboratories studying coronaviruses in the city would have made a mistake leading to emergence of this virus. (This alone raises a few questions for me. Is it unusual for a city the size of Wuhan in China or other countries to have several laboratories with coronaviruses lying around? Or do most big cities have some kind of epidemiological laboratory, and the family of coronaviruses is so common that almost any lab would have examples of it in the fridge? What about the dangerous ones.) They also say definitively this is a natural virus, not a genetically engineered one.

I’ve been to “wet markets” in Singapore and Thailand, which could well be tame compared to the one in Wuhan, I have no idea. I would hypothesize that you have a lot of people working, shopping, and eating in very close proximity to each other. Sometimes you have people doing grosser things, like smoking, or spitting. Cats and dogs sometimes roam freely. And sometimes these markets are air conditioned, I have seen it both ways. So if someone already had the virus, it might have spread between people in the market and have nothing particularly to do with food or wild animals.

But I found it interesting to read what wild animals were actually for sale in the Wuhan market. Do people eat bats, or keep them as pets? (And before you judge as a westerner, be aware people in other cultures are just as horrified by some of our habits and things we eat as we are by some of theirs.)

The so-called wet market had 653 stalls and more than 1,180 employees supplying seafood products as well as fresh fruit and vegetables, meat, and live animals before it closed on Jan. 1, 2020. Days before, 10 stall operators were trading live wild animals, including chipmunks, foxes, raccoons, wild boar, giant salamanders, hedgehogs, sika deer. Farmed, wild and domestic animals were also traded at the market including snakes, frogs, quails, bamboo rats, rabbits, crocodiles and badgers…

Bloomberg

So no bats mentioned. I also find myself thinking about the various “bird flu” and “swine flu” scares of the past. It is often human-livestock contact that gives rise to concerning pathogens, so we should keep that in mind. And of course, there are still plenty of deadly pathogens being spread by mosquitoes, fleas and ticks while we are fixated on this one (admittedly horrific) unusual coronavirus incident.

February 2021 in Review

Most frightening and/or depressing story: For people who just don’t care that much about plants and animals, the elevator pitch on climate change is it is coming for our houses and it is coming for our food and water.

Most hopeful story: It is possible that mRNA technology could cure or prevent herpes, malaria, flu, sickle cell anemia, cancer HIV, Zika and Ebola (and obviously coronavirus). With flu and coronavirus, it may become possible to design a single shot that would protect against thousands of strains. It could also be used for nefarious purposes, and to protect against that are ideas about what a biological threat surveillance system could look like.

Most interesting story, that was not particularly frightening or hopeful, or perhaps was a mixture of both: At least one serious scientist is arguing that Oumuamua was only the tip of an iceberg of extraterrestrial objects we should expect to see going forward.

what a global pandemic/bioweapon surveillance regime could look like

It’s pretty clear that the world needs some kind of surveillance or inspection regime to monitor both biological weapons and natural disease outbreaks. This Wired article goes into some of the possibilities.

  • The WHO is an obvious possibility, but requires full cooperation of member states so this limits what it can do, even if it were well funded.
  • Something like the International Atomic Energy Agency is a possibility. It would have to be established by a treaty and would have the ability to swoop in and inspect advanced biological labs (these are called “biosafety level 4” or BSL-4) on short notice.
  • There is an existing treaty called the Biological Weapons Convention which might have the authority to create this body, but the article says it is somewhat ineffective and a new treaty wouldn’t need to have as many parties, just starting with the major players and letting others sign on over time.
  • Another model is the Organization for the Prohibition of Chemical Weapons, which is similar to IAEA.
  • The UN Security Council would also have the authority to establish a new inspection body, kind of like it did for Iraq in the 1990s (which turned out great… and this is the problem, the UN lost a lot of its previous credibility in that debacle.)

The BSL-4 labs are proliferating around the world according to the article, and this seems like a scary situation to me.

My modest proposal would be to fund the WHO fully right away and have it investigate natural disease outbreaks with member state cooperation. Then have the Security Council establish the heavy-duty biological weapons inspection program with the heavies right away. Like it or not, we also need surveillance to find the hidden labs or even just people messing around with dangerous stuff in their garages and basements. This will be much easier for the little guy to do than, say, getting your hands on some enriched uranium or Novachok.

This is an existential risk – we may not get many chances to make mistakes and learn from them. The risk will keep increasing and under any kind of moral or responsible government framework it has to be dealt with right away.

fun with coronavirus math

Let’s do some coronavirus math! This is a word problem, kids. I’m writing on January 14, 2021, and this post will be horribly outdated, but possibly of historical interest, when you read it.

The total number of cases confirmed to date as of today, in the U.S.: “23.1 million+” (New York Times)

The CDC’s ratio of actual cases to confirmed cases: 7.2 (CDC)

Number of cumulative cases in the U.S. so far: 23.1 million * 7.2 = 166 million (166,320,000)

Population of the United States: 328.2 million (Google)

% of our population that has had the coronavirus = 166 / 328.2 = 51%

% of our population that has been vaccinated: 3.1% (Financial Times)

But all other things being equal (which I am sure they are not), 51% of the people vaccinated will have already had the coronavirus, so the vaccine so far adds 1.6% to 51% of our population. Call it 53% to be generous.

We have heard a variety of estimates on what constitutes herd immunity, but the number 70% seems to be sticking at least in the media (I don’t have a source handy, and need to go do some other things now.) So we might not be that far off. The (painfully) slow but steady vaccine rollout tortoise will eventually get to the finish line, people are continuing to get infected at high rates every day in the meantime, and nobody wants to see another wave from the new variant, but if and when it hits us it might push us over the mark (at a horrific human cost, of course).

One last thought is that at the moment, I suspect we are immunizing people who are more likely to have already had an infection than the population as a whole. We are being told this is the most ethical approach, or the quickest way to lower risk for the population as a whole, or some combination of the two. The ethical statement may be true, although this seems subjective. I thought ethics was not up to ethicists, but rather ethicists were supposed to ascertain what our society as a whole considers ethical, and maybe compare that to other human societies past and present. I haven’t seen public polls of what people think is ethical, although they may exist. I can see a case that the way the vaccine is being rolled out is ethical, but I can also see a case for a random lottery being equally ethical.

Better planning and communication would not just be ethical, they are the common sense need and our government is continuing to fail, fail, fail and people are dying, which is the opposite of ethical governance. To my ears, it is arrogant to hear them lecturing us about ethics.

2020 in Review

2020 has been quite a year for the U.S. and the world, but you don’t need me to tell you that! My work and family life was disrupted, but I have been lucky enough not to lose any family members or close friends to Covid-19 so far. If anyone reading this has lost someone, I want to express my condolences.

Now I’ll get right down to some highlights of my 2020 posts.

Monthly Highlights from 2020

Most frightening or depressing stories:

  • JANUARY: Open cyberwarfare became a thing in the 2010s. We read the individual headlines but didn’t connect the dots. When you do connect the dots, it’s a little shocking what’s going on.
  • FEBRUARY: The Amazon rain forest may reach a tipping point and turn into a dry savanna ecosystem, and some scientists think this point could be reached in years rather than decades. Meanwhile, Africa is dealing with a biblical locust plague. Also, bumble bees are just disappearing because it is too hot.
  • MARCH: Hmm…could it be…THE CORONAVIRUS??? The way the CDC dropped the ball on testing and tracking, after preparing for this for years, might be the single most maddening thing of all. There are big mistakes, there are enormously unfathomable mistakes, and then there are mistakes that kill hundreds of thousands of people (at least) and cost tens of trillions of dollars. I got over-excited about Coronavirus dashboards and simulations towards the beginning of month, and kind of tired of looking at them by the end of the month.
  • APRIL: The coronavirus thing just continued to grind on and on, and I say that with all due respect to anyone reading this who has suffered serious health or financial consequences, or even lost someone they care about. After saying I was done posting coronavirus tracking and simulation tools, I continued to post them throughout the month – for example herehereherehere, and here. After reflecting on all this, what I find most frightening and depressing is that if the U.S. government wasn’t ready for this crisis, and isn’t able to competently manage this crisis, it is not ready for the next crisis or series of crises, which could be worse. It could be any number of things, including another plague, but what I find myself fixating on is a serious food crisis. I find myself thinking back to past crises – We got through two world wars, then managed to avoid getting into a nuclear war to end all wars, then worked hard to secure the loose nuclear weapons floating around. We got past acid rain and closed the ozone hole (at least for awhile). Then I find myself thinking back to Hurricane Katrina – a major regional crisis we knew was coming for decades, and it turned out no government at any level was prepared or able to competently manage the crisis. The unthinkable became thinkable. Then the titans of American finance broke the global financial system. Now we have a much bigger crisis in terms of geography and number of people affected all over the world. The crises may keep escalating, and our competence has clearly suffered a decline. Are we going to learn anything?
  • MAY: Potential for long-term drought in some important food-producing regions around the globe should be ringing alarm bells. It’s a good thing that our political leaders’ crisis management skills have been tested by shorter-term, more obvious crises and they have passed with flying colors…doh!
  • JUNE: The UN just seems to be declining into irrelevancy. I have a few ideas: (1) Add Japan, Germany, India, Brazil, and Indonesia to the Security Council, (2) transform part of the UN into something like a corporate risk management board, but focused on the issues that cause the most suffering and existential risk globally, and (3) have the General Assembly focus on writing model legislation that can be debated and adopted by national legislatures around the world.
  • JULY: Here’s the elevator pitch for why even the most hardened skeptic should care about climate change. We are on a path to (1) lose both polar ice caps, (2) lose the Amazon rain forest, (3) lose our productive farmland, and (4) lose our coastal population centers. If all this comes to pass it will lead to mass starvation, mass refugee flows, and possibly warfare. Unlike even major crises like wars and pandemics, by the time it is obvious to everyone that something needs to be done, there will be very little that can be done.
  • AUGUST: We just had the 15-year anniversary of Hurricane Katrina, a major regional crisis that federal, state, and local governments failed to competently prepare for or respond to. People died, and decades later the recovery is incomplete. Coronavirus proves we learned nothing, as it is unfolding in a similar way on a much larger and longer scale. There are many potential crises ahead that we need to prepare for today, not least the inundation of major cities. I had a look at the Democratic and (absence of a) Republican platforms, and there is not enough substance in either when it comes to identifying and preparing for the risks ahead.
  • SEPTEMBER: The Covid recession in the U.S. is pretty bad and may be settling in for the long term. Demand for the capital goods we normally export (airplanes, weapons, airplanes that unleash weapons, etc.) is down, demand for oil and cars is down, and the service industry is on life support. Unpaid bills and debts are mounting, and eventually creditors will have to come to terms with this (nobody feels sorry for “creditors”, but what this could mean is we get a full-blown financial panic to go along with the recession in the real economy.
  • OCTOBER: Global ecological collapse is most likely upon us, and our attention is elsewhere. The good news is we still have enough to eat (on average – of course we don’t get it to everyone who needs it), for now.
  • NOVEMBER:  It seems likely the Clinton-Bush-Obama-Trump U.S. foreign wars may just grind on endlessly under Biden. Prove us wrong, Joe! (I give Trump a few points for trying to bring troops home over the objections of the military-industrial complex. But in terms of war and peace, this is completely negated and then some by slippage on nuclear proliferation and weapons on his watch.)
  • DECEMBER: The “Map of Doom” identifies risks that should get the most attention, including antibiotic resistance, synthetic biology (also see below), and some complex of climate change/ecosystem collapse/food supply issues.

Most hopeful stories:

  • JANUARY: Democratic socialism actually does produce a high quality of life for citizens in many parts of the world. Meanwhile, the hard evidence shows that the United States is slipping behind its peer group in many measures of economic vibrancy and quality of life. The response of our leaders is to tell us we are great again because that is what we want to hear, but not do anything that would help us to actually be great again or even keep up with the middle of the pack. This is in the hopeful category because solutions exist and we can choose to pursue them.
  • FEBRUARY: A proven technology exists called high speed rail.
  • MARCH: Some diabetics are hacking their own insulin pumps. Okay, I don’t know if this is a good thing. But if medical device companies are not meeting their patient/customers’ needs, and some of those customers are savvy enough to write software that meets their needs, maybe the medical device companies could learn something.
  • APRIL: Well, my posts were 100% doom and gloom this month, possibly for the first time ever! Just to find something positive to be thankful for, it’s been kind of nice being home and watching my garden grow this spring.
  • MAY: E.O. Wilson is alive and kicking somewhere in Massachusetts. He says if we want to save our fellow species and ourselves, we should just let half the Earth revert to a natural state. Somewhat related to this, and not implying my intellect or accomplishments are on par with E.O. Wilson, I have been giving some thought to “supporting” ecosystem services in cities. When I need a break from intellectual anything, I have been gardening in Pennsylvania with native plants.
  • JUNE: Like many people, I was terrified that the massive street demonstrations that broke out in June would repeat the tragedy of the 1918 Philadelphia war bond parade, which accelerated the spread of the flu pandemic that year. Not only does it appear that was not the case, it is now a source of great hope that Covid-19 just does not spread that easily outdoors. I hope the protests lead to some meaningful progress for our country. Meaningful progress to me would mean an end to the “war on drugs”, which I believe is the immediate root cause of much of the violence at issue in these protests, and working on the “long-term project of providing cradle-to-grave (at least cradle-to-retirement) childcare, education, and job training to people so they have the ability to earn a living, and providing generous unemployment and disability benefits to all citizens if they can’t earn a living through no fault of their own.”
  • JULY: In the U.S. every week since schools and businesses shut down in March, about 85 children lived who would otherwise have died. Most of these would have died in and around motor vehicles.
  • AUGUST: Automatic stabilizers might be boring but they could have helped the economy in the coronavirus crisis. Congress, you failed us again but you can get this done before the next crisis.
  • SEPTEMBER: The Senate Democrats’ Special Committee on the Climate Crisis had the courage to take aim at campaign finance corruption as a central reason for why the world is in its current mess. I hate to be partisan, folks, but right now our government is divided into responsible adults and children. The responsible adults who authored this report are the potential leaders who can lead us forward.
  • OCTOBER: We have almost survived another four years without a nuclear war. Awful as Covid-19 has been, we will get through it despite the current administration’s complete failure to plan, prevent, prepare, respond or manage it. There would be no such muddling through a nuclear war.
  • NOVEMBER: The massive investment in Covid-19 vaccine development may have major spillover effects to cures for other diseases. This could even be the big acceleration in biotechnology that seems to have been on the horizon for awhile. These technologies also have potential negative and frivolous applications, of course.
  • DECEMBER: The Covid-19 vaccines are a modern “moonshot” – a massive government investment driving scientific and technological progress on a particular issue in a short time frame. Only unlike nuclear weapons and the actual original moonshot, this one is not military in nature. (We should be concerned about biological weapons, but let’s allow ourselves to enjoy this victory and take a quick trip to Disney Land before we start practicing for next season…) What should be our next moonshot, maybe fusion power?

Most interesting stories, that were not particularly frightening or hopeful, or perhaps were a mixture of both:

  • JANUARY: Custom-grown human organs and gene editing and micro-satellites, oh my!
  • FEBRUARY: Corporate jargon really is funny. I still don’t know what “dropping a pin” in something means, but I think it might be like sticking a fork in it.
  • MARCH: I studied up a little on the emergency powers available to local, state, and the U.S. federal government in a health crisis. Local jurisdictions are generally subordinate to the state, and that is more or less the way it has played out in Pennsylvania. For the most part, the state governor made the policy decisions and Philadelphia added a few details and implemented them. The article I read said that states could choose to put their personnel under CDC direction, but that hasn’t happened. In fact, the CDC seems somewhat absent in all this other than as a provider of public service announcements. The federal government officials we see on TV are from the “Institute of Allergies and Infectious Diseases”, which most people never heard of, and to a certain extent the surgeon general. I suppose my expectations on this were created mostly by Hollywood, and if this were a movie the CDC would be swooping in with white suits and saving us, or possibly incinerating the few to save the many. If this were a movie, the coronavirus would also be mutating into a fog that would seep into my living room and turn me inside out, so at least there’s that.
  • APRIL: There’s a comet that might be bright enough to see with the naked eye from North America this month. [Update: It wasn’t. Thanks, 2020.]
  • MAY: There are unidentified flying objects out there. They may or may not be aliens, that has not been identified. But they are objects, they are flying, and they are unidentified.
  • JUNE: Here’s a recipe for planting soil using reclaimed urban construction waste: 20% “excavated deep horizons” (in layman’s terms, I think this is just dirt from construction sites), 70% crushed concrete, and 10% compost.
  • JULY: The world seems to be experiencing a major drop in the fertility rate. This will lead to a decrease in the rate of population growth, changes to the size of the work force relative to the population, and eventually a decrease in the population itself.
  • AUGUST: Vehicle miles traveled have crashed during the coronavirus crisis. Vehicle-related deaths have decreased, but deaths per mile driven have increased, most likely because people drive faster when there is less traffic, absent safe street designs which we don’t do in the U.S. Vehicle miles will rebound, but an interesting question is whether they will rebound short of where they were. One study predicts about 10% lower. This accounts for all the commuting and shopping trips that won’t be taken, but also the increase in deliveries and truck traffic you might expect as a result. It makes sense – people worry about delivery vehicles, but if each parcel in the vehicle is a car trip to the store not taken, overall traffic should decrease. Even if every 5 parcels are a trip not taken, traffic should decrease. I don’t know the correct number, but you get the idea. Now, how long until people realize it is not worth paying and sacrificing space to have a car sitting there that they seldom use. How long before U.S. planners and engineers adopt best practices on street design that are proven to save lives elsewhere in the world?
  • SEPTEMBER: If the universe is a simulation, and you wanted to crash it on purpose, you could try to create a lot of nested simulations of universes within universes until your overload whatever the operating system is. Just hope it’s backed up.
  • OCTOBER: There are at least some bright ideas on how to innovate faster and better.
  • NOVEMBER: States representing 196 electoral votes have agreed to support the National Popular Vote Compact, in which they would always award their state’s electoral votes to the national popular vote winner. Colorado has now voted to do this twice. Unfortunately, the movement has a tough road to get to 270 votes, because of a few big states that would be giving up a lot of power if they agreed to it.
  • DECEMBER: Lists of some key technologies that came to the fore in 2020 include (you guessed it) mRNA vaccines, genetically modified crops, a variety of new computer chips and machine learning algorithms, which seem to go hand in hand (and we are hearing more about “machine learning” than “artificial intelligence” these days), brain-computer interfaces, private rockets and moon landings and missions to Mars and mysterious signals and micro-satellites and UFOs, virtual and mixed reality, social media disinformation and work-from-home technologies. The wave of self-driving car hype seems to have peaked and receded, which probably means self-driving cars will probably arrive quietly in the next decade or so. I was surprised not to see cheap renewable energy on any lists that I came across, and I think it belongs there. At least one economist thinks we are on the cusp of a big technology-driven productivity pickup that has been gestating for a few decades.

That’s a lot to unpack, and I’m not sure I can offer a truly brilliant synthesis, but below are a few things that are on my mind as I think through all this.

We Americans affirmed that we care about our parents and grandparents (then failed to fully protect them).

One thing I think we learned is that we still value human lives more than a cold, purely economic calculation might suggest, including the lives of our elderly parents and grandparents. (Though we had significant failures of execution when it came to actually protecting people – more on that later.) We have had this debate before in the U.S., for example when thinking about how much to invest in environmental and safety regulations as I was reminded of by this Planet Money podcast. At one point, politicians (can you guess from which party) proposed valuing the lives of senior citizens at lower rates than everyone else. The backlash was fierce and instant, and the proposal was withdrawn. This year, we did not really have that debate – it was simply accepted, for the most part, that we would be willing to endure significant economy-wide pain to try to protect our parents and grandparents.

I kind of liked how Mr. Money Mustache put it back in April. He gave a “worst case scenario” with 3 million deaths and a “best case scenario” with 200,000 deaths, and the reality is on track to be somewhere in between.

In the worst case, our public officials would all downplay the risk of COVID-19, and we’d keep working and traveling and spreading it freely. We’d maximize our economic activity and let the disease run its course…

In the more compassionate case which we are currently following, we drastically reduce the amount of contact we have with each other for a few months, which cuts the number of deaths in the US down from 3-6 million, down to perhaps 200,000. In exchange, our economy shrinks by several trillion dollars (it was about 21 trillion in 2019) for a year or more.

Assuming we are preventing 3 million early deaths, this means our society is foregoing about one million dollars of economic activity for each person’s life that we extend and frankly, it makes me happy to know we are capable of that.

Mr. Money Mustache

The leaders of some countries like Russia, Brazil, and even Sweden seem to have chosen to accept the consequences of business as usual. Most other countries have chosen to try to save human lives at the expense of short-term economic activity, and some executed this strategy much more effectively than others. In the U.S. and UK, we seem to be bumbling idiots who feel some compassion for one another.

The United States has been slipping for awhile, and in 2020 we faltered.

The U.S. continues to slip below average among its developed country peers in many statistical categories like life expectancy, violence, incarceration, suicide, poverty, and public infrastructure. I picture us like a horse that used to be leading the race, then slipped into the middle of the leading pack, and has now drifted toward the back of the leading pack and is continuing to lose ground. Keep slipping and we would no longer be part of the leading pack.

But then came Covid-19, our horse faltered, and all the other horses went thundering past, leaving us in last place. With the possible exception of the UK, we had the least effective response in the world. Like I said, I think a few countries like Russia, Brazil, and Sweden basically chose to accept the consequences of a limited response, and that is different than a failed response (though not to the people who died or whose loved ones died). We tried to respond, and it turned out our government was unprepared and incompetent even compared to developing countries.

So what happened? Some particular failing of the Anglo-American countries doesn’t explain it, because Canada and Australia both did pretty well. Our lack of a public health system (or even universal access to private care) doesn’t explain it, because the UK, Canada, and Australia all have similar systems to each other and divergent outcomes.

The difference between the extraordinary low rates in Asia, and the higher rates in Europe and the Americas is particularly stark. There are a couple things that I think may explain it. First is good airport screening. I traveled in Asia during the swine flu pandemic, and the screening is robust. The U.S. obviously has to beef up its health infrastructure at international airports and other border crossings (yes, there is a certain irony here that is lost on anti-immigrant types.) Part of this is also beefing up the data systems that track who is coming in from where, where they are going and what their status is. It became obvious within weeks that the CDC’s databases were a complete failure.

I think beyond border screening and data management, the other big difference between East and West is that Asian countries were willing to restrict physical movement and enforce quarantine, whereas western countries mostly were not. Had I exhibited symptoms while I was traveling in Singapore or Thailand during the swine flu, either country would have detained me in a government facility (with three meals a day and wi-fi, one would hope) for 14 days. Asian countries have also been willing to shut down domestic airports, train systems, and highways at times. Most western countries are simply not willing to do this. In the U.S., I think it is partly a matter of law and politics, but also a stupid idea that it would be “too expensive” when quite obviously it would have saved trillions of dollars in the long run. We simply don’t have the political will, the institutional mechanisms, or the basic competence. Covid-19 was a borderline crisis – a lot of people will lose cherished parents and grandparents but it is not an existential threat to our country’s survival. The U.S. needs to plan now to quarantine effectively in an even worse pandemic or god forbid, an incident involving biological weapons.

A few words on government agencies. Hurricane Katrina came up a few times in the monthly picks above. That was a major failure of federal, state, and local governments in the U.S. to plan, respond, and rebuild after a disaster. Before that, I would have assumed FEMA was up to the task, as they seem to have been in the past. Most people’s faith in the CDC was similar or even greater, and they turned out to be bumbling fools. The U.S. will need to fund its public agencies, stock them with competent, well-trained technocrats, and appoint talented political leaders to integrate them with the rest of society if they are going to function competently in the future.

In a hurricane, FEMA basically rolls into your city and takes charge, for better or worse. Early on, there was speculation that the CDC might try to do something similar in a disease outbreak. That didn’t happen. We will also need to adequately fund and train state and local agencies, if we are going to continue to put the lion’s share of the burden on them in a decentralized disaster like this. We could just get rid of the states and have the federal government work directly with metro areas, but this seems like a pretty pie in the sky idea politically.

What other government agencies do we have faith in that might have turned into rotten hollow logs while we weren’t paying attention? The Treasury and Federal Reserve do in fact seem to know what they are doing, which has saved us a couple times now in the last couple decades. We assume the military can fight a war if they need to. We assume the Department of Agriculture can feed us. Are we sure?

The democratization of propaganda.

Governments in general, and the U.S. government in particular, are having trouble getting messages out to their citizens. We used to worry about governments and big business controlling the media to put out purely ideological or purely profit-driven messages. Now anyone in the world can pretty much say anything anytime. People have trouble telling which messages are truthful and which are more reliable than others. In the U.S., this is combined with low trust in government and low trust in experts, and the result is that people either didn’t receive important messages about public health, or received a variety of conflicting information and noise and didn’t reach reasonable conclusions reading to reasonable decisions.

We hear a lot about “following the science” and “listening to scientists”, but this is really about policy communication not science communication. Scientists are trained to communicate uncertainty to each other. Often though, the uncertainty is low enough that it is clear one course of action has better odds of a good outcome than others. Media do not communicate this well – they tend to focus on the uncertainty statements scientists make, even when uncertainty is low and the best course of action is clear. The public is not prepared to process this information in a way that will lead to reasonable conclusions and decisions.

So we need to try to educate children to evaluate the source of information and think critically about whether it makes sense in the context of what they know. We need to educate them about uncertainty and decision making. We need to train journalists better to communicate scientific information but especially policy choices. Regulating social media companies might play some small role in this, but in the U.S. at least we don’t want to see a move toward censorship.

Back to the CDC. When Covid-19 hit, I was expecting the CDC to step in and dominate communications from the beginning on the issue. They needed to use all the tools modern advertising has to get messages across. I would have trusted what they said, and I think a lot of people would. If they had seized the initiative, it would have been hard for other voices to compete, and we might be in a better place now. Unfortunately, they have probably suffered a permanent loss of credibility both through poor communication and inadequate action, but better communication would definitely have helped. Make this one more U.S. institution that has lost credibility in my eyes as I have gotten older – Congress, the State Department, and the New York Times after weapons of mass destruction (I never trusted intelligence agencies), the military after the failures in Afghanistan and Iraq (I’m not saying I trusted them per se, but I thought they were good at fighting wars), FEMA after Hurricane Katrina (and more recently the horrific non-response in Puerto Rico), and now the CDC and federal public health establishment.

I have come to respect local public health authorities more through all of this. I actually work in the same building as my local public health agency, and know some people who work there, but I never really saw the connection to the larger health care system or my daily life before this. Part of the federal government’s communication strategy should be to package crystal clear messages for delivery by trusted local individuals like public health workers, family doctors, and school nurses.

Preparing for the big (and small) risks

Covid-19 has caused me to think even more about risk management. A major pandemic was something we knew was virtually certain to happen at some point, and we knew the consequences could be severe. And yet we still failed to adequately plan, prepare, and respond. There are a few other things in this category, like (obviously) another pandemic, a major earthquake, and sea level rise. Then there are risks where we are not sure of the probability, but the consequences could be catastrophic, like nuclear and biological war, ecological collapse, and major food shortages. (Alien invasion? No, I’m not really taking this seriously, but along with things like “gray goo” it should be on the list and discussed, providing a rational basis for taking action or not.) Then there are things that are certain to happen but are geographically limited (storms, fires, floods) or steadily kill a few people here and there adding up to a lot over time (car crashes, air pollution, poor nutrition). I am not sure where some risks fit in, for example cyberattacks or antibiotic resistance – but this is the point of gathering the information and having the discussions in a rational framework. In a rational world, a risk management framework provides a way to allocate finite resources (money, effort, expertise, research) to planning, preparing, mitigating, or simply choosing to accept each of these.

The state of scientific and technological progress (is the Singularity near yet?)

I had a decent technology list under “most interesting post” for December, so I won’t repeat it here.

Above, I find myself referring to the Covid vaccine as a “moon shot”. It is clearly an example of how a big government push can get a new technology over the finish line and bring it into widespread use quickly. I am wondering though if it is a true example of accelerating a scientific breakthrough, an example of accelerating application of a scientific breakthrough to new technology, or simple a case of government correcting a market failure. We had been hearing about mRNA vaccine technology for awhile, and we know a vaccine was developed for SARS but not widely deployed. We have also been hearing for awhile that drug companies were still growing basic childhood vaccines in chicken eggs, and not investing heavily in the mRNA technology, because the market demand and profit potential was not there in the rich countries to make it worth their while. So this was at least partially a case of the U.S. and other governments making that market failure go away by simply paying for everything and simply transferring the profits to those companies. I am not saying this is bad – we do it for arms manufacturers all the time, so why not vaccines?

Vaccines for HIV, dengue fever and other similar mosquito-borne diseases would be nice. One solution to antibiotic resistance might be bacteriophages – viruses tailored specifically to infect and kill specific bacteria. It seems like this technology could be applied to this. If antibiotic resistance is really the medium- to long-term emergency some say it is, maybe this should be a top priority.

This technology is also scary. It is the ability to create a custom organism that can go into a person’s body and have a specific desired effect. Vaccines are obviously a benign application, but somebody, somewhere, sometime will use this technology for evil. This seems like a near-existential risk on the horizon that needs to be dealt with.

I am going to say no, the Singularity is not imminent in 2021. Then again, the idea is that if at some point we hit the knee of the curve on technology and productivity, it will seem to accelerate all at once, because that is the nature of exponential change. If that happens, we will shrug and say we knew it all along. The trick is to find ways to drive innovation and progress while managing the risks that could temporarily but repeatedly set back or permanently derail that path, and without destroying our planetary ecosystem in the process. I am not ready to put odds on what outcome we are headed for, but I am hoping 2021 will at least bring a gradual return to the pre-Covid status quo, and allow us to set the stage for the future.

If anyone has actually read my ramblings all the way to this point, or just skipped to the end, Happy New Year!

humidity helps reduce coronavirus transmission

Humidify those schools!

The relationship between climatic factors and COVID‐19 cases in New South Wales, Australia was investigated during both the exponential and declining phases of the epidemic in 2020, and in different regions. Increased relative humidity was associated with decreased cases in both epidemic phases, and a consistent negative relationship was found between relative humidity and cases. Overall, a decrease in relative humidity of 1% was associated with an increase in cases of 7–8%. Overall, we found no relationship with between [sic] cases and temperature, rainfall or wind speed.

Transboundary and Emerging Diseases

Not being a scientist or doctor, I have always assumed that mucous membranes inside your nose help block germs, and that a dried out nose in the winter time is one reasons colds, coughs, and flu spread through schools and offices every winter. It seems like a relatively simple measure to take that would have a clear positive effect. Now, to sit back and wait for my children’s schools and my office building manager to explain why it can’t be done.

Covid Act Now

This is a new site that gives a Covid risk rating based on five indicators: daily new cases, infection rate, test positivity, ICU headroom, and contacts traced. They try to give the same information by county, but they only have the data to provide a couple of the indicators at the county level. I know this data exists for my county, but it must be collected and stored (or not) differently in different counties and different states, so that there is no single organized database of it. This is the kind of thing the federal government could provide leadership on, and once again, they are just failing us in epic fashion.

I’ve added this to my running list of Covid data and simulation sites.

U.S. still isn’t screening international arrivals!

In looking for that explanation of why some countries have largely dodged the coronavirus bullet while the U.S. is melting down, many people are focused on masks. I wonder if the almost total failure to screen airport arrivals could be the single most important factor. Thousands of plane loads of infected people from Italy landed in the U.S. northeast airports in February and March. The CDC’s screening and tracking protocols completely broke down, and it got out of control before there was any chance to contain it. Fast-forward to June, and they still aren’t effectively screening airport passengers!

Then we arrived in the US. No one at Dulles International Airport checked passengers’ temperatures. SAA had given each passenger health forms to fill in for the US authorities. No one asked for them. No sanitisers were on offer. No social distancing was practised in the immigration queues. People literally breathed down my neck. In Joburg the 2m apart rule was strictly observed.

At the immigration counter my passport was stamped and the very nice border policeman said: “Welcome to America.”

I waltzed over to baggage reclaim, got my luggage and left. I could have walked into the US coughing, sweaty and feverish and not a single authority would have known — they hadn’t bothered to do a basic check that I wasn’t indeed feverish.

JUSTICE MALALA: What three American airports taught me about Covid-19 and political leadership

Before it gets to the U.S. arrival, the article recounts the strict measures in place in South Africa (“one of the nations Trump included in the class of “shithole countries” – direct quote from the article). I’m not familiar with this person or publication, by the way, but it matches my experience traveling in Southeast Asia (Singapore and Thailand specifically) during the 2009 swine flu epidemic. Temperature screening and screening questionnaires were everywhere, beginning the moment I arrived at an airport, and continuing in shopping centers, on public transportation, etc. It was all polite and professional, but I knew that if I developed symptoms I would be taken to a government-run quarantine center for 14 days. (And as long as they had three meals a day and a decent internet connection, that didn’t sound like the end of the day!) Thailand and Singapore have both handled this pandemic very well. Thailand in particular is a middle income country with (until recently) a lot of back and forth travel to Wuhan, China.

You can argue that the “second wave” or “second peak” horror show now unfolding in the U.S. can be pinned on poor state and local leadership, but the early failures of airport screening, tracking, and testing were squarely on the federal government’s shoulders, and they not only failed spectacularly compared to most other countries, they haven’t learned anything!

coronavirus trackers and simulations revisited

Update: December 13, 2020 (and from time to time since then, I update links if I notice they are broken)

This post is getting a surprising amount of attention. I don’t normally update posts, but I am updating this one since it is getting attention and the commentary in the original post is significantly outdated. Rest assured, if you are a historian in the far future studying what I was thinking back in June 2020, I have kept the original post at the bottom. I am keeping all the links, just grouping them somewhat and removing (from this section) the outdated commentary. (Thank you, Word Press, for making a simple copy-and-paste operation like this beyond excruciating.)

Data Trackers

  • Johns Hopkins – map, stats, access to data sets
  • New York Times – a national (U.S.) map by county and plots by state (now, with a paywall! as of 7/30/21. Which I will never pay because WEAPONS OF MASS DESTRUCTION!)
  • Financial Times – similar to others, but they look at excess deaths a little differently and have some interesting graphics
  • BBC – similar to NYT, but international
  • CDC – changed this link to their “COVID-19 by County” page on 2/26/22; the updated recommendation is to mask indoors if new cases in your county are 200,000 per 100,000 population per week, AND if the number of people entering the hospital and/or in the hospital is above certain thresholds. It’s a little hard to find the data and figure out yourself, so if you trust the CDC (and who wouldn’t?) you can just type in your county and they will tell you if it is high/medium/low.
  • https://coronavirus.thebaselab.com/ – a variety of maps and plots
  • City Observatory – intermittent data-based articles and maps
  • Our World in Data – excellent interactive country-level data, maps, and plots. A tip – you can also type in “world” or the name of a continent in the country box.
  • https://aatishb.com/covidtrends/ – a very clever animated time series of growth in cases over time, by country
  • Reuters – just more numbers and maps, similar to NYT
  • Covid Act Now – state-level data and communication in a simple, easy to understand index format
  • Harvard Global Health Institute COVID Risk Levels Dashboard – similar to Covid Act Now, but less simple and less easy to understand. Seems to have more ability to drill down into county-level data, although when you do that much of it is blank.
  • Wastewater surveillance from “Biobot Analytics” – added 4/30/22.

Simulations

  • University of Washington IHME – the best place I have found for understandable future projections. At the state level.
  • FiveThirtyEight – compares different models (no longer updating as of 7/30/21)
  • https://covid19risk.biosci.gatech.edu/ – This site calculates the probability that someone in a group of a given size is infected, based on the estimated rate of active cases in a U.S. state.
  • MicroCOVID – a risk calculator based on local data and allowing you to adjust your risk tolerance and try out various scenarios (added 8/8/21), such as “one night stand with a random person” (on the latter, please remember there are other diseases besides just Covid-19, for example antibiotic-resistant syphilis…)
  • Covid-19 Forecast hub – another visualization of various models and ensembles of models

Vaccine Trackers

Local Pennsylvania/Philadelphia Interest

  • The state of Pennsylvania has a useful dashboard which they have now made public (or it was public before and I didn’t notice.) It compares cases, positive tests, and hospital data for the current and last 7-day period, at the county level.
  • Speaking of Philadelphia, a shout out to the Philadelphia Health Department which provides some open downloadable data.

Miscellaneous Stuff

Original Post (June 27, 2020)

I decided to list out and summarize the variety of trackers and simulations I’ve mentioned in previous posts. Like many people (in the U.S. Northeast at least), I was glued to coronavirus info on various screens from roughly mid-March to mid-May, then my attention started to gradually drift to other things as the situation got better. Now, it seems that it has either stabilized at a not-quite-out-of-the-woods level, or is slowly reversing itself as we see other parts of the country start to be affected more seriously (sorry if you are reading this and are being affected, we in the Northeast take no pleasure in your suffering, I promise, although we suggest you turn out any bigoted anti-science politicians in your area who are letting this happen.) Anyway, I find that I am interested in starting to look at trackers and simulations again on a daily basis. These are in the order I discovered them.

  • Johns Hopkins – a neat map early on, although now the entire world has become a blob. Still a good place to stare at data.
  • New York Times – a national (U.S.) map by county and plots by state. seems to load even though I have used all my free articles for the month.
  • BBC – they update continuously but I’m not sure if this link will be to the latest
  • CDC – this is what I would have predicted would be the go-to source of information and expertise if you asked me before all this started…but it’s mediocre at best. Yes, that just about sums it up.
  • https://coronavirus.thebaselab.com/ – a variety of maps and plots to stare at, not my first stop but a little different if I am tired of others
  • University of Washington IHME – still the most informative state-level simulations I have found, accounting for hospital capacity among other things
  • City Observatory – they did an awesome analysis by U.S. metro area, which I have not seen anyone else do (human beings interact with each other socially and economically in cities and their suburbs, which often cut across states, and states often contain metro areas that are not connected much socially or economically. Economists, social scientists and urban planners know this of course, but nobody else studying the epidemic seems to have figured this out. Seriously, other data visualization and simulation sites, you can do this, it’s just a matter of grouping data by counties.) Unfortunately, they quit updating it and have not automated it. I still check every now and then to see if they have picked it up.
  • Our World in Data – pretty much every conceivable way of looking at data by country. I like to look at confirmed deaths per million across countries. By this measure, the starkest contrast is east vs. west. The eastern countries were hit first, hard, and without warning, and their death rates are very, very low. They have a variety of government types, responses, ethnicities and cultures. I just don’t think anybody has come close to explaining it. The U.S. is in the middle of the pack of western countries, which somewhat contradicts conventional wisdom and suggests news organizations are making the obvious error of not normalizing by population.
  • https://aatishb.com/covidtrends/ – an animated time series of new confirmed cases in the past week vs. total confirmed cases, both on a log scale, by country. As I write this, shows the beginning of a concerning uptick for the United States, and Brazil out of control.
  • Reuters – I actually never wrote about this one, but it has a map and some numbers.
  • FiveThirtyEight – they have an aggregation of various simulation models out there. New York and New Jersey look like a stream sprayed horizontally out of a garden hose, while Texas and Florida (today) look more like a fire hose.
  • https://covid19risk.biosci.gatech.edu/ – This site calculates the probability that someone in a group of a given size is infected, based on the estimated rate of active cases in a U.S. state. I assume it’s estimated active cases, anyway, or it wouldn’t make sense. It would be better by metro area (seriously guys, someone just get this done), but still a nice idea. I’m in Philadelphia, but I figure the New Jersey numbers are probably the most applicable.
  • Covid Act Now – provides a composite risk index at the state level, and county when county level data is available in the right format (which is not that often)
  • Harvard Global Health Institute COVID Risk Levels Dashboard – keeps it simple with just data on new cases, but gives you a variety of nice mapping, charting, and tabular formats to slice and dice the data at country, (U.S.) state or county level.
  • The state of Pennsylvania has a useful dashboard which they have now made public (or it was public before and I didn’t notice.) It compares cases, positive tests, and hospital data for the current and last 7-day period, at the county level.
  • Speaking of Philadelphia, a shout out to the Philadelphia Health Department which provides some open downloadable data.
  • I look at the FAO food price index on occasion. It’s falling lately. Sometimes I look at oil and gold prices, and how many Special Drawing Rights can be bought with one U.S. dollar. Oh and, the Rapture Index is at an all time high!