You implement preventive measures before the problem worsens, Governor Walz

The numbers of the infected are surging in Minnesota, so now our governor says “Whoops!” and decides maybe we should refrain from wild partying.

Gov. Tim Walz strongly indicated during the Monday opening of a new saliva testing center in Minneapolis that he will soon announce restrictions on bars and restaurants as a way of stemming an explosion of COVID-19 infections in Minnesota.

Walz stood with Health Commissioner Jan Malcolm to announce another expansion in testing, this time at the Minneapolis Convention Center, but both officials further lamented an increase in both infection numbers and positivity rates. The state saw 10,000 new infections over the weekend and passed a 10 percent positivity rate.

Walz said health department information is seeing three infection sources: social events such as weddings and funerals, large family gatherings and bars and restaurants. The latter dovetails into another concern of health officials — the large number of 18-to-35 years olds who may be infected but asymptomatic. Those people can be efficient spreaders.

Barn doors, closed, after cow escapes, etc. OK. I think the citizenry have already learned to be slack about these things, unfortunately, and there is also going to be a subset of the population — you know the ones, the conspiracy theorists — who are going to see this as a validation of their belief that the Democrats want to steal muh freedoms.

In more positive news, I’ve been reading the news about the new potential vaccine. It’s an RNA-based vaccine? Cool. That’s an intriguing approach, except for the fact that RNA is remarkably fragile. My concerns were confirmed by this little bit of information:

Pfizer’s vaccine must be stored at ultra-low temperatures, which complicates the massive endeavor to distribute a vaccine throughout the population. Pfizer’s logistical plan includes using dry ice to transport frozen vials. Health facilities can keep the vaccine for up to six months at minus-70 degrees Celsius, or minus-94 degrees Fahrenheit. But many hospitals lack the special freezers that can get that cold.

So that’s like dry ice temperatures, but at least it’s not liquid N2 temperatures. I guess that’s doable, but it’s going to add to the expense and mostly force communities to upgrade their medical infrastructure a bit. Otherwise, though, the idea of using RNA to put the patient’s immune system to work making viral antigens is just kind of brilliant. I hope it’s working soon, and that maybe Governor Walz gets ahead of the game this time and starts making grants to regional medical institutions so they’re ready as soon as the vaccine is available.

Yeah, and closing the bars would have been a brilliant idea, too…last month.

Adam Savage on hearing loss

He gives a good answer to a common question.

My hearing is fine, thank you very much, except for an obnoxious tinnitus that isn’t yet affecting my life much. My wife, however, is losing her hearing in an unusual way, with the lower registers progressively dropping out (usually it’s the other way around, losing the higher frequencies first). Savage mentions the high cost of hearing aids, and we have some experience with that — there’s a reason for it. Modern hearing aids aren’t just amplifiers that make all sounds louder, they have to be more sophisticated than that. For instance, my wife has an app on her phone that lets her tweak the amplification, it’s like a built-in equalizer so she can boost the volume at specifically the frequencies that are affected. The technology is cool, but Savage is right — it’s also awkward and clumsy and expensive.

At least her condition means my voice is becoming gradually more inaudible, while she can hear the grandkids just fine, which is probably for the best. It still ought to be a right for everyone to have this kind of necessary support. You never know, maybe someday I’ll say something worth listening to!

I wonder which of the fervent Republicans at the rally infected him?

You know, Herman Cain attended a Trump rally maskless, and proudly posted a photo of himself hanging out with a small crowd of people, also maskless, and then was diagnosed with COVID-19 afterwards.

Now Herman Cain is dead of COVID-19.

Please, please, please take the pandemic seriously. Even you Republicans. It’s real. It kills people. Even people you might like.

Deborah Birx’s reputation will never recover

Which is only fair, since her enabling of Trump is a catastrophe from which the nation will never recover. The NY Times has a piece on how Trump failed the pandemic test, and Birx plays a prominent role in it.

For scientific affirmation, they turned to Dr. Deborah L. Birx, the sole public health professional in the Meadows group. A highly regarded infectious diseases expert, she was a constant source of upbeat news for the president and his aides, walking the halls with charts emphasizing that outbreaks were gradually easing. The country, she insisted, was likely to resemble Italy, where virus cases declined steadily from frightening heights.

On April 11, she told the coronavirus task force in the Situation Room that the nation was in good shape. Boston and Chicago are two weeks away from the peak, she cautioned, but the numbers in Detroit and other hard-hit cities are heading down.

A sharp pivot soon followed, with consequences that continue to plague the country today as the virus surges anew.

In April. I remember April. Did anyone think we were on the right path in April? We’d shut down my university, but already I was seeing people refuse to accept it, clamoring to get back to bars and beaches.

Dr. Birx was more central than publicly known to the judgment inside the West Wing that the virus was on a downward path. Colleagues described her as dedicated to public health and working herself to exhaustion to get the data right, but her model-based assessment nonetheless failed to account for a vital variable: how Mr. Trump’s rush to urge a return to normal would help undercut the social distancing and other measures that were holding down the numbers.

Yeah, models built on assumptions, like that Americans wouldn’t be stupid, and that Trump wouldn’t encourage that stupidity. Just the fact that Donald Trump is president should tell you how wrong that is.

Inside the White House, Dr. Birx was the chief evangelist for the idea that the threat from the virus was fading.

Unlike Dr. Fauci, Dr. Birx is a strong believer in models that forecast the course of an outbreak. Dr. Fauci has cautioned that “models are only models” and that real-world outcomes depend on how people respond to calls for changes in behavior — to stay home, for example, or wear masks in public — sacrifices that required a sense of shared national responsibility.

Again, a responsible nation would not have elected Donald Trump.

Dr. Birx’s belief that the United States would mirror Italy turned out to be disastrously wrong. The Italians had been almost entirely compliant with stay-at-home orders and social distancing, squelching new infections to negligible levels before the country slowly reopened. Americans, by contrast, began backing away by late April from what social distancing efforts they had been making, egged on by Mr. Trump.

The difference was critical. As communities across the United States raced to reopen, the daily number of daily cases barely dropped below 20,000 in early May. The virus was still circulating across the country.

Italy’s recovery curve, it turned out, looked nothing like the American one.

Nope. Because Italians were smarter than Americans…or rather, I should say, Italians didn’t have failed leaders who were modeling the worst possible behavior for containing the infection, and didn’t have scientists feeding their delusions.

Other nations had moved aggressively to employ an array of techniques that Mr. Trump never mobilized on a federal level, including national testing strategies and contact tracing to track down and isolate people who had interacted with newly diagnosed patients.

“These things were done in Germany, in Italy, in Greece, Vietnam, in Singapore, in New Zealand and in China,” said Andy Slavitt, a former federal health care official who had been advising the White House.

“They were not secret,” he said. “Not mysterious. And these were not all wealthy countries. They just took accountability for getting it done. But we did not do that here. There was zero chance here that we would ever have been in a situation where we would be dealing with ‘embers.’ ”

We could still take those actions that other nations did — in fact, we really ought to, despite the fact that it’s late and those measures will cost more and we’re still going to suffer the tragic consequences of our failures — but we won’t. Classes start in a month, and my university still plans on opening, and I’m going to have to teach in-person labs, and students will still be moving into the dorms, and will still be gathering in the cafeterias for meals as a group, and will probably still be heading out to the bar for quarter taps on Thursday nights. It’s madness. If the University of Minnesota had asked me, I would have told them to slam on the brakes right now, refuse to enable the massing of students in one place, and teach online classes only for a year. The summer of 2021 would be the time to discuss cautiously reopening fully, but only if the pandemic was under control.

Nobody asked me. I was only told to prepare a plan for a limited reopening, not asked whether we should open at all.

At least I’m not a Birx making happy-clappy PowerPoints to show how everything is going to be just fine. When I’m feeling optimistic, I put the chances of me being dead within a year at about 10%.

The COVID-19 crisis is an opportunity for charlatans on all sides

I’d never heard of Surgisphere before. Apparently, no one had. They just suddenly appeared out of nowhere with vast amounts of data from numerous hospitals, a gigantic database that they’d used to address the question of the utility of hydroxychoroquine in treating COVID-19, and came back with the expected answer: no, it’s not any good. They got quoted all over the place! Great PR! Suddenly, lots of people had heard of Surgisphere.

Unfortunately, Surgisphere is a crock.

The World Health Organization and a number of national governments have changed their Covid-19 policies and treatments on the basis of flawed data from a little-known US healthcare analytics company, also calling into question the integrity of key studies published in some of the world’s most prestigious medical journals.

A Guardian investigation can reveal the US-based company Surgisphere, whose handful of employees appear to include a science fiction writer and an adult-content model, has provided data for multiple studies on Covid-19 co-authored by its chief executive, but has so far failed to adequately explain its data or methodology.

Data it claims to have legitimately obtained from more than a thousand hospitals worldwide formed the basis of scientific articles that have led to changes in Covid-19 treatment policies in Latin American countries. It was also behind a decision by the WHO and research institutes around the world to halt trials of the controversial drug hydroxychloroquine. On Wednesday, the WHO announced those trials would now resume.

Hey! Nothing wrong with citizen input from science fiction writers and adult-content models. There had better be more substance behind the claims, though. It turns out that there is confusion about how many employees the company has (100? 6? 3?) depending on the source, there don’t seem to be any people with the special skills need for the study — this is Big Data stuff, lots of statistics and computer science — and the data has been falling apart. The study claimed to be derived from “96,000 patients with Covid-19, admitted to 671 hospitals from their database of 1,200 hospitals around the world”, but various hospitals have reported that the data doesn’t match what they’ve reported.

And then, the big question: how did this company get access to so much confidential medical information?

One of the questions that has most baffled the scientific community is how Surgisphere, established by Desai in 2008 as a medical education company that published textbooks, became the owner of a powerful international database. That database, despite only being announced by Surgisphere recently, boasts access to data from 96,000 patients in 1,200 hospitals around the world.

When contacted by the Guardian, Desai said his company employed just 11 people [nobody seems to know how many people work there]. The employees listed on LinkedIn were recorded on the site as having joined Surgisphere only two months ago. Several did not appear to have a scientific or statistical background, but mention expertise in strategy, copywriting, leadership and acquisition.

What is clear is that there was a massive falsification of data. It also looks like the chief executive of the company, Sapan Desai, is a con artist with a history of pseudoscientific schemes.

What’s interesting about the story, though, is that it demonstrates how everyone is a bit gullible, and is willing to suspend skepticism a bit when the science, pseudo or otherwise, seems to support prior expectations. Lots of people got fooled by this one. Researchers even suspended ongoing trials because they thought Surgisphere had just provided the definitive answer! At first, it was only the hydroxychloroquine fanatics who were skeptical of the study, and embarrassingly, they were right, in this one case. But the real difference is that the real scientists, like David Gorski, will reassess their conclusions in the light of new information, admit to their error, and move on.

That’s the difference between the cultists and me. I’ll change my mind if they present new information that checks out when I dig into it. It’s also a lesson that a believer’s skepticism when examining something he disagrees with will always be far more rigorous than when looking at a study that goes against what he currently believes. Think of it as a somewhat embarrassing reminder to myself (coupled, perhaps, with a bit of self-flagellation) to remain humble in the future and not to be too fast to dismiss criticisms coming from even the cultists.

Surgisphere’s papers are getting trashed. The legitimate hydroxychloroquine studies have resumed — way too many studies than the treatment deserves, if you ask me. If they come back with positive information about the value of the drug (I don’t think they will, since the claims all originated from sources as quacky as Sapan Desai) then I’ll accept new treatment recommendations. The question is, will the drug’s proponents accept any evidence from any studies that show its efficacy is baseless?

The realistic perspective

My university has closed all face-to-face classes until 1 April, when, I presume, they’ll reassess what should be done. I hope no one thinks everything will be over then, because it won’t be. We’re just getting started. I expect April is when the pandemic in the US will be just roaring into action.

Some experts agree.

40-70% of the US population will be infected over the next 12-18 months. After that level you can start to get herd immunity. Unlike flu this is entirely novel to humans, so there is no latent immunity in the global population.
[We used their numbers to work out a guesstimate of deaths— indicating about 1.5 million Americans may die. The panelists did not disagree with our estimate. This compares to seasonal flu’s average of 50K Americans per year. Assume 50% of US population, that’s 160M people infected. With 1% mortality rate that’s 1.6M Americans die over the next 12-18 months.]
The fatality rate is in the range of 10X flu.
This assumes no drug is found effective and made available.
The death rate varies hugely by age. Over age 80 the mortality rate could be 10-15%.
Don’t know whether COVID-19 is seasonal but if is and subsides over the summer, it is likely to roar back in fall as the 1918 flu did

There is no guarantee that this will be a replay of the 1918 pandemic, but we should prepare as if it is. I’m teaching cell biology in the fall, I’m going to spend the summer getting organized for possibly having to teach it online.

I hope that’s all I have to do, and we’re not going to end up preparing by digging trenches for mass graves.

This next recommendation is personally bothersome. My wife flew to Colorado before the extent of the crisis became unavoidably obvious. She was supposed to fly back next week. Flying is out of the question anymore, so we’ve been trying to come up with alternative methods of getting her back home.

We would say “Anyone over 60 stay at home unless it’s critical”. CDC toyed with idea of saying anyone over 60 not travel on commercial airlines.

Right now we’re considering that instead maybe she should stay in Boulder with my daughter for some indefinite period of time. Safety apart is smarter than travel together that maximizes our chance of infection.

“Stop testing.”

They started testing for SARS-CoV-2 in Seattle, with one researcher, Helen Chu, leading the way. They started getting positive hits, and then the federal government stepped in, but not to anyone’s benefit.

The state laboratory, finally able to begin testing, confirmed the result the next morning. The teenager, who had recovered from his illness, was located and informed just after he entered his school building. He was sent home and the school was later closed as a precaution.

Later that day, the investigators and Seattle health officials gathered with representatives of the C.D.C. and the F.D.A. to discuss what happened. The message from the federal government was blunt. “What they said on that phone call very clearly was cease and desist to Helen Chu,” Dr. Lindquist remembered. “Stop testing.”

I found that shocking. Stop collecting information, stop responding to patient concerns, minimize the threat. This is not what I want the government to do.

On a phone call the day after the C.D.C. and F.D.A. had told Dr. Chu to stop, officials relented, but only partially, the researchers recalled. They would allow the study’s laboratories to test cases and report the results only in future samples. They would need to use a new consent form that explicitly mentioned that results of the coronavirus tests might be shared with the local health department.

They were not to test the thousands of samples that had already been collected.

While I sympathize with privacy concerns, this is a situation where public health ought to have priority. Being diagnosed with COVID-19 does not create a permanent stigma. It guides the appropriate response to the affected individual.

Especially since this is what’s happening:

In the days since the teenager’s test, the Seattle region has spun into crisis, with dozens of people testing positive and at least 22 dying — many of them infected in a nursing home that had unknowingly been suffering casualties since Feb. 19.

My mother lives in that area, she’s a few years older than I am (just a few), and she’s already had a few respiratory episodes that required temporary hospitalization. When I talked to her the other day, she’s self-quarantining and avoiding going out in public at all…but I feel like if there were a problem, she wouldn’t get the help she would need, but instead is going to be told to shut up.

Michigan State University suspends all face-to-face classes

Uh-oh. Given that move, I’m expecting dictates from on high at my university any day now.

Also Ohio.

Oh. And Minnesota.

“While the Duluth, Rochester and Twin Cities campuses are on Spring Break this week, and in anticipation of the Crookston and Morris campus breaks next week, we encourage our faculty to begin preparing to move classroom instruction online, especially for courses where this can be implemented immediately,” University of Minnesota-Twin Cities President Joan Gabel wrote in a letter to students, faculty, and staff Tuesday.

“Encourage” is different from “ordering”. I’m going to talk to my students in class about this today.

Add my alma mater, the University of Washington, to the list. Although I see that the Seattle Mariners are still dithering about their sporting events. Will it wipe out all the sportsball fans who go into crowded stadiums next?

What will I do if a virus closes my classes?

Yikes. I just read this comment about the coronavirus shut down in Poland — 22 cases in the whole country, so all university classes are suspended for the next month. That’s taking the issue seriously and taking major steps to slow the spread of the disease.

At my university, it’s only provosts and deans and chancellors and department heads talking about contingency plans, with no imminent threat of a shut down. But it could happen! With the number of cases doubling every week, I might come back from Spring Break to find my students have been ordered to stay away. I’ve scribbled up a quick contingency plan for my genetics course, just in case.

Contingency plan for Genetics (Biol 4312)

Genetics is an unusual lab course in that it already doesn’t fit the mold of the weekly intensive lab session. We’re working with Drosophila, and are at the mercy of their 9 day reproductive cycle, so we have to be more flexible. Typically, we meet for a half hour to an hour at the scheduled lab time, during which I explain the steps that the students need to take that week. The students need to come in frequently during the course of that week to maintain their flies, set up crosses when they’re ready, and count phenotypes. Some weeks this is a light load, coming once or twice on their own time to check on flies; other weeks they may have to come in 3 or 4 times a day to collect flies for a cross; and on several occasions they have to come in for long sessions of fly screening. The variability and flexibility suggest one fairly non-disruptive way to protect students.

Staggered, scheduled lab times. To minimize exposure, I could set up specific, individual lab times for each student. Right now, it’s a free-for-all with students doing their work whenever they can, but we could switch to exclusive lab sessions for each. So far this semester we have completed one whole experiment involving 3 different crosses, so students are familiar with the details of the methods, and they are experienced enough to not need direct instruction from me; I could manage with an explicit set of detailed instructions on Canvas for the steps in the next experiment.

They would still be using a shared lab facility, so we’d couple this scheduling with instructions on using sanitizers and sterilizing lab benches with alcohol between students.

In a worst case scenario, in which the university is shut down, another alternative is:

Drosophila genetics kits. I could assemble a kit with two fly stocks, a half dozen fly bottles, a small supply of medium, some anesthetic, and a hand lens for each student or pair of students. They could then carry out the whole experiment at home, again with detailed week-by-week instructions on Canvas. Data would be shared between students online.

Potential problems: Lack of an incubator would mean developmental rates might vary significantly. A hand lens is going to make it harder for students to score phenotypes. Currently, if one student’s cross fails, they can share specimens with other students and complete the experiment; in isolation, if one cross fails, they’ll be unable to finish. The final assays are somewhat labor intensive, alleviated by the fact that a group can share the load of counting thousands of flies.

Please note that these alternatives are only feasible because the students have completed an experiment with multiple crosses in the first half of the semester, with direct instruction and demonstration from me on how to set up a cross, how to maintain flies, and how to analyze phenotypes. The second half of the semester is repeating these same methods with a very different kind of cross and different mutant phenotypes. These stop-gap procedures would not be applicable to teaching a full semester lab course in fly genetics.

Setting up staggered lab times looks like wishful thinking now, if entire countries are locking out universities in the face of the threat. I might have to spend my spring break boxing up flies and media for distribution.