Monthly Archives: March 2020

Regarding John Ioannidis my correspondent remarks …

Ioannidis is an interesting guy who has played a great part in the retraction of many medical research papers over the last 15 years. https://www.theatlantic.com/…/lies-damned-lies…/308269/

And that certainly puts him up a couple of points in my book, too. A quote from The Atlantic article:

That question has been central to Ioannidis’s career. He’s what’s known as a meta-researcher, and he’s become one of the world’s foremost experts on the credibility of medical research. He and his team have shown, again and again, and in many different ways, that much of what biomedical researchers conclude in published studies—conclusions that doctors keep in mind when they prescribe antibiotics or blood-pressure medication, or when they advise us to consume more fiber or less meat, or when they recommend surgery for heart disease or back pain—is misleading, exaggerated, and often flat-out wrong. He charges that as much as 90 percent of the published medical information that doctors rely on is flawed. His work has been widely accepted by the medical community; it has been published in the field’s top journals, where it is heavily cited; and he is a big draw at conferences. Given this exposure, and the fact that his work broadly targets everyone else’s work in medicine, as well as everything that physicians do and all the health advice we get, Ioannidis may be one of the most influential scientists alive. Yet for all his influence, he worries that the field of medical research is so pervasively flawed, and so riddled with conflicts of interest, that it might be chronically resistant to change—or even to publicly admitting that there’s a problem.

I still am bothered by the lack of nuance in the Stat article, but I’ll put it down to size constraints. And this won’t make him – or me – happy:

Health officials in New York City and Los Angeles County are signaling a change in local strategy when it comes to coronavirus testing, recommending that doctors avoid testing patients except in cases where a test result would significantly change the course of treatment.

A news release from the Los Angeles Department of Public Health this week advised doctors not to test those experiencing only mild respiratory symptoms unless “a diagnostic result will change clinical management or inform public health response.”

The recommendation reflects a “shifting from a strategy of case containment to slowing disease transmission and averting excess morbidity and mortality,” according to the statement.

The guidance said coronavirus testing at L.A. County public health labs will prioritized those with symptoms, health care workers, residents of long-term care facilities, paramedics and other high-risk situations. Others are encouraged to simply stay at home. [CNN]

This loss of information will make it harder to understand the virus & associated disease, from immediate infection to long term consequences. And there’s at least one article I’ve run across that suggests there are two variants at work here:

When Xiaolu Tang at Peking University in Beijing and colleagues studied the viral genome taken from 103 cases, they found common mutations at two locations on the genome. The team identified two types of the virus based on differences in the genome at these two regions: 72 were considered to be the “L-type” and 29 were classed “S-type”.

A separate analysis by the team suggests that the L-type was derived from the older S-type. The first strain is likely to have emerged around the time the virus jumped from animals to humans. The second emerged soon after that, says the team. Both are involved in the current global outbreak. The fact that the L-type is more prevalent suggests that it is “more aggressive” than the S-type, the team say.

I like the abstraction inherent in this tree, but I fear the photo failed to capture it.

I should have moved in closer and cut off the bottom houses and cars.

Just hours after I wondered about the data coming out of Africa with regard to the COVID-19 pandemic, I ran across this article in NewScientist (14 March 2020) which may provide some answers:

African countries are both vulnerable and potentially more resilient to the coronavirus. On the one hand, the population is much younger than in Europe and China. The median population age in the UK is 40.2 and in China it is 37, but this figure is 17.9 in Nigeria, Africa’s most populous country. “If you look at the statistics from China, the people that have worse prognosis are the older people, not necessarily the young,” says Stephen.

They also suggest at least some of the African nations are vigilant about incoming visitors.

I had also noted Russia’s small reported numbers. Its median age? 39.6, comparable to the UK & China. CNN has a report today on Russia’s small reported numbers, and it feels properly confusing, as Russia often can be:

“The director-general of WHO said ‘test, test, test,'” Dr. Melita Vujnovic, the World Health Organization’s representative in Russia, told CNN Thursday. “Well, Russia started that literally at the end of January.”

Vujnovic said Russia also took a broader set of measures in addition to testing.

“Testing and identification of cases, tracing contacts, isolation, these are all measures that WHO proposes and recommends, and they were in place all the time,” she said. “And the social distancing is the second component that really also started relatively early.”

Rospotrebnadzor, Russia’s state consumer watchdog, said Saturday that it had run more than 156,000 coronavirus tests in total. By comparison, according to CDC figures, the United States only picked up the pace in testing at the beginning of March, while Russia says it has been testing en masse since early February, including in airports, focusing on travelers from Iran, China, and South Korea. …

Anastasia Vasilyeva, a doctor for Russian opposition figure Alexey Navalny and leader of the Alliance of Doctors union, made headlines with a series of videos in which she claims the authorities are covering up real coronavirus numbers by using pneumonia and acute respiratory infection as a diagnosis.

“You see they said the first coronavirus patient that died, that the cause of death was thrombosis,” Vasilyeva told CNN. “That’s obvious, nobody dies from coronavirus itself, they die from the complications, so it’s very easy to manipulate this.”

Moscow health officials denied the accusation and said they were testing pneumonia patients for coronavirus. The WHO’s Dr. Vujnovic also was skeptical about Vasilyeva’s claim.

“If there was a hidden, unrecognized burden somewhere it would be seen in these [pneumonia] reports,” she said. “So I do not believe this is happening, which does not say that you might not see an increase of cases in the next period, because we have seen that in many countries.”

I have no idea what to make of this. Cover up? So competent they make us look like a clown herd?

Finally, a reader sends this link to a site named Stat, with which I’m unfamiliar. The article bemoans the general uncertainty of knowledge concerning COVID-19, but I have to wonder if they think the professionals at the CDC are dunces. Then I ran across this paragraph:

The one situation where an entire, closed population was tested was the Diamond Princess cruise ship and its quarantine passengers. The case fatality rate there was 1.0%, but this was a largely elderly population, in which the death rate from Covid-19 is much higher.

Perhaps the writer, John Ioannidis, is a victim of bad editing, or perhaps he doesn’t understand how to analyze the situation. Here’s the error as I see it: He’s taking age as a fundamental factor in determining risk.

It’s not.

Age is a proxy for making general statements about underlying health conditions. In general, the aged have less effective immune systems than do the young. But a proxy is always a step away from the fundamentals, and so when using a proxy, one must always view it with some slight suspicion, applying caveats of both qualitative and quantitative measures.

The health professionals have been at pains to emphasize that any sort of underlying health condition may put those who’ve contracted the virus at risk for a severe episode. These constitute the fundamental factors of the risk.

Taking Ioannidis’ paragraph as an example, once you realize age is a proxy, then you find a set of questions that need to be answered:

• Are elderly cruise line passengers more or less likely to be as healthy as the median elderly person in the population? If it’s more healthy, then adjust the derived rates for severe and terminal episodes up; if it’s less healthy, then adjust the derived rates down. By derived, I mean the absolute rate for elderly persons, regardless of context.
• How does the level of care delivered on a cruise ship compare to that at an average 1^st world hospital? I’ve never taken a cruise, so I am clueless.
• How did caring for infected cruise line passengers impact other non-infected hospitalized passengers?
• How did the stress of being at sea, with limited resources, impact the recovery of infect passengers? In particular, the psychological stress of having home countries turn your ship away – a dreaded plague ship, as it were – must take a toll on patients of a certain range of temperaments.
• Etc.

Some folks may view the cruise liner situation as an excellent isolated experiment, but I have my doubts that at least Ioannidis’ article understands the nuances of the situation, based on the toss-off nature of that paragraph. And I do get that precision to 15 decimal places is useless, but it would help to at least say, within a magnitude, how COVID-19 compares to the seasonal flu.

Watching the Trump Administration inevitably reminds me of the brutal Soviet government, which insistently saw everything through the lens of politics, even to the extent of attaching political officers to military units. Now, I’m not saying that’s literally happening here, not at all, but this Steve Benen report on Maddowblog concerning the upcoming release of employment figures, until now a source of joy for the Trump Administration, sent up red flags for me:

Ahead of the next report, which will be released next week, the Trump administration is reportedly asking states not to release their own preliminary tallies. The New York Times reported, “In an email sent Wednesday, the Labor Department instructed state officials to only ‘provide information using generalities to describe claims levels (very high, large increase)’ until the department releases the total number of national claims next Thursday.”

It’s not yet clear if state officials will go along.

It sure sounds to me like political management of what is simply a harsh reality.

Look, many readers will just shrug and claim a Democratic Administration would have done the same thing, and perhaps, under some hypothetical Democrats, it would have. But that’s just a form of the discredited argument called uh-whataboutism, which I find more and more reasons to ignore.

One of the lovely things about democracies is that, when properly run, people can learn to trust the government. This President personally has 16,000+ non-distinct lies, prevarications, and boasts to his name, and an Administrative record full of shame when it comes to foreign relations (migrant children in cages, extortion of foreign leaders, toadying to other foreign leaders), etc etc. Most Americans don’t trust him.

So when the Labor Department issues “instructions” to state officials, which I doubt it has any legal authority to do so, to hold back on details of their State’s employment situation, I have to think this is going to be all about the spin.

If Trump and his Administration had a record of honest dealing with the electorate, then we wouldn’t see this, and we wouldn’t have to consider whether or not we should simply disregard the upcoming release of the numbers as being possibly fallacious or whatever. We could simply say, Yes, it’s the COVID-19 response causing this, and it’s just some pain we’ll have to bear, and it’s good to see the Administration is trying to help those who’ve lost jobs.

Trump could have so easily spun it to his advantage in the upcoming elections. But, instead, he lies through his teeth constantly. This is what liars reap.

For those readers who had their hopes pinned on how the Earth circles the sun as explaining the warm up in temperatures, in particular based on this study in Scientific Reports, I have some bad news:

A prominent scientific journal has retracted a study claiming that climate change was due to solar cycles rather than human activity.

Last year, Scientific Reports came under fire for publishing a paper that researchers said made elementary mistakes about how Earth moves around the sun.

Today the journal, published by Nature Research, which also has Nature in its stable of titles, formally retracted the paper by a team at UK universities and an institution in Azerbaijan.

The withdrawn study had argued that the average global 1°C temperature rise since the pre-industrial period was due not to humanity’s greenhouse gas emissions but to the distance between Earth and the sun changing over time as the sun orbits the barycentre, the solar system’s centre of mass. In a statement today, Scientific Reports said that was inaccurate. …

“Solar system orbital dynamics is extremely well understood, and it wouldn’t have taken much for the authors to have checked if their claims about the significance of the motion of the sun around the solar system barycentre were indeed correct,” [Astronomy Professor Ken Rice at the University of Edinburgh, UK] says. [NewScientist, 14 March 2020]

Which casts shade on the rest of the paper. If you click on the link to the study, it’s prominently marked as RETRACTED.

And, yes, at least one of the authors is upset:

Valentina Zharkova at the University of Northumbria, one of the paper’s authors, says the retraction was unfair and the corrections made to the paper were minor.

Apparently, the experts disagreed and made a convincing case to the editors of Scientific Reports.

A reader writes concerning how Italy has recently passed China in number of deaths from COVID-19:

Apparently there are a lot of Chinese nationals living and working for Chinese-owned factories in northern Italy, and a lot of travel back and forth for the Chinese New Year holiday: https://www.newyorker.com/…/the-chinese-workers-who…

That explains a lot – basically, northern Italy becomes a small province of China. But are we seeing the same thing in Africa, which also has some significant transitory Chinese populations? From the image on the right, it appears not – but, again, how trustworthy is the data? All those small dots mean a very small number of infections, and no deaths.

And Russia continues to have absurdly small numbers.

Source: Wikipedia

Way back when, comets were viewed with superstitious dread. They were considered harbingers of disaster, pestilence, doom and –

Ah, yes. Like what we’re going through now.

So Spaceweather has this report, which is rather like adding a pedestrian to a crosswalk in a movie. It’s decorative, goes with the mood, all that sort of thing.

COMET ATLAS IS BRIGHTENING FASTER THAN EXPECTED: Get ready for a wild ride. Comet ATLAS (C2019 Y4) is plunging toward the sun and, if it doesn’t fly apart first, it could become one of the brightest comets in years.

“Comet ATLAS continues to brighten much faster than expected,” says Karl Battams of the Naval Research Lab in Washington DC. “Some predictions for its peak brightness now border on the absurd.”

The comet was discovered in December 2019 by the Asteroid Terrestrial-impact Last Alert System (ATLAS) in Hawaii. Astronomers quickly realized it might be special. On May 31, 2020, Comet ATLAS will pass deep inside the orbit of Mercury only 0.25 AU from the sun. If it can survive the blast furnace of solar heating, it could put on a good show.

However, no one expected the show to start this soon. More than 2 months before perihelion (closest approach to the sun), Comet ATLAS is already “heating up.” The worldwide Comet Observation Database shows it jumping from magnitude +17 in early February to +8 in mid-March–a 4000-fold increase in brightness. It could become visible to the naked eye in early April.

Keep an eye out. I’m not superstitious and I’ve love to see a big ol’ comet.

As the COVID-19 pandemic closes much of the service and entertainment industries and renders superfluous, hopefully temporarily, many jobs in said industries, our social system is feeling the strain:

As Americans turn to unemployment insurance, some are finding they do not qualify. Or if they do, the average payment of $385 a week is modest. In some states, there is a week-long waiting period before the first payment arrives.

“Workers expect unemployment insurance to be there for them in a downturn. A bunch of workers are about to find out that it’s not,” said Martha Gimbel, a labor economist at Schmidt Futures who was formerly at Indeed.com. “This is a real-life nightmare. Every hole we allowed to grow in our social safety net is hitting us all at once.” …

Many economists are urging Congress to quickly boost funding for state unemployment insurance. The Families First Coronavirus Response Act that President Trump signed Wednesday included $1 billion to help states with administrative costs of processing unemployment insurance, but additional stimulus will be needed to cover more people. Twenty-three states were already running low on money in their unemployment trust funds before the pandemic hit. [WaPo]

If I were one of those searching for and not finding unemployment benefits, I’d be asking Where does the responsibility lie? And while I haven’t done the research to discover that, it seems likely the GOP, legendarily parsimonious with unemployment benefits, and well-known to have, as a minor religious tenet of the Party, the belief that everyone would refuse to work if they could get away with it, bears some responsibility.

Since the Democrats will be asking it, let’s ask ourselves: is it valid for the Democrats, stipulating that the Republicans are mostly guilty of rending the social safety net, to use these failures as an attack vector during the various campaigns over the summer?

No doubt the guilty will scream NO!, but I think it is a valid political question.

Look: it is the responsibility of government to provide for disasters and emergencies. The private sector has neither the authority nor the ability to coordinate for the various needs and requirements, and its motivations make it ill-suited to try. The government must be prepared and adequately funded for disasters. If it’s not, then either the disaster is beyond imagining – and, despite President Trump’s ribald attempts to claim the answer is that it was beyond imagining, it was really on the radar of disaster specialists for decades – or someone or some group is a systemic failure.

And there’s no reason that the political enemies of the screwups shouldn’t take advantage of it; indeed, it would be a dereliction of duty to not do so.

And, hey, if the Democrats are the responsible Party, then the Republicans should be at their throats, instead.

But in the end, a disaster doesn’t make the associated political questions invalid. After all, we should be all about preventing them, not rationalizing them.

From the Centers for Disease Control:

FIGURE 2. Coronavirus disease 2019 (COVID-19) hospitalizations,* intensive care unit (ICU) admissions,† and deaths,§ by age group — United States, February 12– March 16, 2020

* Hospitalization status missing or unknown for 1,514 cases.
† ICU status missing or unknown for 2,253 cases.
§ Illness outcome or death missing or unknown for 2,001 cases.

Perhaps the 20-40 year olds think it’ll be a lark to get COVID-19, but stays in the ICU are never pleasant, or so I gather from family members who’ve done so.

That said, there’s something else to bear in mind: for survivors of COVID-19, we have no idea, apparently and expectedly, of the long-term consequences of infection. It’s not unknown for pathogens to have long-term effects, even if the victim survives the acute phase. For example, measles can cripple your immune system:

The toll of measles on the immune system

Many of the deaths attributable to measles virus are caused by secondary infections because the virus infects and functionally impairs immune cells. Whether measles infection causes long-term damage to immune memory has been unclear. This question has become increasingly important given the resurgence in measles epidemics worldwide. Using a blood test called VirScan, Mina et al. comprehensively analyzed the antibody repertoire in children before and after natural infection with measles virus as well as in children before and after measles vaccination. They found that measles infection can greatly diminish previously acquired immune memory, potentially leaving individuals at risk for infection by other pathogens. These adverse effects on the immune system were not seen in vaccinated children. [“Measles virus infection diminishes preexisting antibodies that offer protection from other pathogens,” Michael J. Mina, et al, Science]

Perhaps survivors of COVID-19 become sterile, have diminished cognitive capacities, or some other life-defining problem.

Treating COVID-19 as nothing more than a minor flu may be more costly than you youngsters – get off the lawn beach! – think.

Here we are on the set of Game of Thrones, folks. Please don’t meddle with the stage pieces. [Sotto voce: Damn kids. I should never have taken this position as tour guide.]

What could possibly go wrong?

Yet, in Knives Out (2019), Harlan Thrombey, master of the murder mystery form, is found with his throat slit and the knife still in his hand the next morning, and the fun begins. Between children who’ve been sucking at his teat for their entire lives, grandchildren twisted by their parents, and faithful nurse Marta, there’s no shortage of suspects.

Into this delightful mess strides private detective Benoit Blanc, an American of non-specific Southern extraction (actually, my Arts Editor gagged a little on the actor’s accent), hired anonymously to travel to Massachusetts and assist the local police in the investigation into what appears to be a suicide.

Slowly, methodically, and quietly, he begins to unravel the story presented, not realizing there’s not one, but two deceptions clouding the view.

But the lead here is nurse Marta, the Ecuadoran who may be here legally, but her Mom’s not. Who may have been Harlan’s best friend, but is doing horrible things for him. Sort of horrible. Maybe horrible?

And looking at a bleak future, paved in green paper. You were wondering? Of course you were. And she hates it.

Knives Out doesn’t hit all the targets. The gratuitous use of shock is ineffective – so the grandkid is a Nazi who pleasures himself in odd places, that’s just not really a big shock, but then today’s culture specializes in shock. A second victim, well, I didn’t even recognize her, and I was paying attention. She should have been given some sort of distinguishing characteristic. A third eye, poor taste in art, SOMETHING.

But the storytellers do have their clever moments, and I won’t spoil them except to say I did enjoy the opening sequence of police interviews. It’s not unique, but it’s well done and gives a bit of insight into all these family members.

There may not be anything profound in Knives Out, but the plot didn’t seem to have any holes in it, bad people got some sort of comeuppance, and it was a fun way to spend a couple of hours. Just don’t worry about his mother, or who the hell was the mother of all these kids. Maybe they popped out of Harlan’s forehead. Or something equally scandalous.

Some minor bits of news for you Senate campaign fans out there.

• The Republican March 31st Alabama primary run-off contest between favored Tommy Tuberville and former holder of the Senate seat Jefferson Beauregard Sessions III has been postponed until July 14. It’ll be interesting to see if the rivals continue to flay each other, thus alienating the opposition’s supporters, or if a temporary truce is called. If the former occurs, look for Senator Jones (D) to increase his chances of retaining the seat.
• The same NBC News story also reports “Five other states also have postponed their primaries because of the coronavirus pandemic: Georgia, Kentucky, Louisiana, Maryland and Ohio.” However, Kansas is not, but the Democrats are urging voters to use mail-in ballots.
• Senator Dick Durbin (D-IL) now knows his Republican opponent: former Lake County Sheriff Mark Curran. There’s still little to suggest Durbin will face a tough challenge.

… is that you then draw questionable conclusions, questionable further questions, and other such adventures in FallacyLand. So consider this:

Yeah. Russia, with a population of 144 million, or very roughly one tenth of its neighbor China, has no deaths.

Really?

And I have heard nary a word on the subject.

I wonder if epidemiologists are adjusting for possibly bad data out of Russia.

Meanwhile, Italy, with a population of 60 million, is nearly at 3,000 deaths, which is very near China’s totals. Again, how trustable is this data?

Jeroboam:

1. A wine bottle holding 3 liters (approximately 0.8 gallon) of sparkling wine.
2. A wine bottle holding 4.5 liters (approximately 1.2 gallons) of still wine. [The Free Dictionary]

Noted in “America’s germaphobes were ready for this — and have been for too long,” Karen Heller, WaPo:

Baker suffers from health anxiety disorder, also known as hypochondriasis. Obsessive-compulsive disorder, or OCD, is its frequent companion. Germs are the mortal enemy. Tony Shalhoub’s detective character in “Monk,” with his phobia of unclean surfaces and bountiful supply of sanitary wipes, is the disorder’s poster child.

Baker’s home is never without end-times supplies of bleach, hydrogen peroxide and the twin set of germ weaponry in our newly confined world order, dainty bottles of hand sanitizer and jeroboams of disinfecting wipes.

Senator McConnell (R-KY), leader of the Senate but in trouble in his reelection race, is looking for a bit of leeway from his probable opponent:

U.S. Senate Majority Leader Mitch McConnell’s campaign called on a potential Democratic opponent — former Marine Corps pilot Amy McGrath — to stop running political advertisements during the COVID-19 pandemic.

“Amy McGrath’s decision to blanket the airwaves with deceitful ads during the coronavirus outbreak is tasteless and shameful,” said McConnell campaign manager Kevin Golden. “As Kentuckians adjust their daily lives and schedules to help stem the outbreak, the last thing they need to see on TV is negative political advertising. The McGrath campaign must stop airing all of their advertisements.”

McGrath has been running advertisements in Kentucky since July, when she first announced her campaign for U.S. Senate. Recently, she has been running national ads on MSNBC and Fox News in an effort to boost her already prolific fundraising totals. [Lexington Herald-Leader]

Meanwhile, in Ohio …

Dr. Harriet Hall, M.D., nails something I’ve often implied but never have discussed or generalized in the article “In Praise Of Uncertainty“, (Skeptical Inquirer, Volume 44, Issue 2, paywall):

I have often thought that certainty is the root of all evil, or at least the biggest problem facing humanity. A few years ago, two women came to my door. I didn’t talk to them long enough to find out which religion they were proselytizing for, but I was intrigued by their approach. They asked if I knew what the biggest problem facing the world today was, and I answered that it was certainty, people who were absolutely sure they were right about something. They agreed with me, saying, “I know just what you mean.” They didn’t realize I was talking about them.

Uncertainty is the admission that acquiring absolute and exact knowledge about the world is a difficult thing. Uncertainty, more importantly, is the acknowledgment that being strongly wrong can lead to profound disaster, whether we’re talking investing, engineering, the mind of the divine, or marriage.

It’s the boat labelled I Know God Loves Me that sets sail ill-prepared and sinks tragically. It’s the car with the bumper sticker I Know Better that hits the innocent child while the driver, secure in his superior knowledge, chitters away on the phone. It’s the pride and disdain that we all hate, and yet so many of us practice ourselves.

It’s why I’m an agnostic, not an atheist. It’s why I view all knowledge, and all of my opinions, as tentative and contingent on future knowledge, subject to verification.

It’s really at the center of this report by Steve Benen on the pride of the incoming Trump Administration cabinet and staffers:

Donald Trump’s presidential transition period was an unusually chaotic period. To be sure, the crash-course process is difficult for even the most prepared and well-organized operations, but the Republican’s team struggled more than most. As Inauguration Day approached, the incoming administration simply wasn’t prepared to govern.

That was not for lack of effort on the part of the outgoing Obama administration. The week before Trump took the oath of office, Obama’s team prepared an exercise in which the incoming team was presented with a series of hypothetical scenarios — including one in which the world faced a deadly viral outbreak — and how the U.S. federal government would have to respond. …

In theory, the session should’ve helped prepare the Trump administration for the crisis that’s currently unfolding. In practice, it didn’t quite work out that way. …

Another element to this was the Republican officials’ belief that Obama’s team had nothing of value to offer them and made little effort to learn from the outgoing officials before taking office.

While the Politico article on which Benen’s opinion piece is based is somewhat less condemnatory, it still makes clear the attitude of the incoming Trump Administration officials: high and mighty, coming off their bizarre win over Clinton, certain … oh so certain … that they knew better than Obama’s professionals.

We’ve seen how that has worked out, haven’t we? That is, if my reader hasn’t confined their reading to conservative Trump-rah-rah sites.

Hall really wraps up the entire philosophy of uncertainty with a bow and presents it as the position superior to those believe they possess the truth – or, at least, willing to sell themselves that way. And I like it.

DARPA, the American agency Defense Advanced Research Projects Agency, progenitor of the Internet and GUIs, among other things, is still at it. It would seem they’ve taken notice of reproducibility issues, as Nature reports:

In 2016, the US Defense Advanced Research Projects Agency (DARPA) told eight research groups that their proposals had made it through the review gauntlet and would soon get a few million dollars from its Biological Technologies Office (BTO). Along with congratulations, the teams received a reminder that their award came with an unusual requirement — an independent shadow team of scientists tasked with reproducing their results.

Thus began an intense, multi-year controlled trial in reproducibility. Each shadow team consists of three to five researchers, who visit the ‘performer’ team’s laboratory and often host visits themselves. Between 3% and 8% of the programme’s total funds go to this independent validation and verification (IV&V) work. But DARPA has the flexibility and resources for such herculean efforts to assess essential techniques. In one unusual instance, an IV&V laboratory needed a sophisticated US$200,000 microscopy and microfluidic set-up to make an accurate assessment.

The key here is Biological technology. This sort of thing is already being done for hardware and software:

Engineers expect their work to be subject to an IV&V process, in which the organization conducting the research uses a separate set of engineers to test, for example, whether microprocessors or navigation software work as expected. NASA’s IV&V facility was established more than 25 years ago and has around 300 employees testing code and satellite components.

I’m not entirely clear as to whether they refer to what I think of as QA (Quality Assurance), which consists of a collection of engineers and testers who try to make sure the software does what it’s designed to do without going off the rails. The description of this process sounds more advanced:

The synthetic-biology focus of DARPA’s Biological Control programme is well suited to merging biological research with reproducibility studies. The programme aims to bring engineering principles of design and control to biology. By definition, this requires the adoption of best practices from the engineering community — such as IV&V — to improve the likelihood that technologies can advance.

Awardees were told from the outset that they would be paired with an IV&V team consisting of unbiased, third-party scientists hired by and accountable to DARPA. In this programme, we relied on US Department of Defense laboratories, with specific teams selected for their technical competence and ability to solve problems creatively. To get comfortable with the concept of IV&V, investigators needed reassurance that replicating teams would not steal ideas or derail publications. They also needed to get used to their results being challenged even before peer-review submission, and they needed reminders that cooperating with these teams was a programme requirement.

It sounds fascinating. I hope they rotate the scientists through the various teams, both to vitiate hard feelings and to properly give all the team members to opportunity to learn all the techniques. In my experience, no one knows everything, and sometimes it can be quite an eye-opener to see how someone else solved a problem.

Casey Dreier of The Planetary Society reports on the latest budget request from the President, including a puzzling – or sad – reduction in funding:

The President’s Budget Request (PBR) for NASA’s next fiscal year was released on 10 February. And while the $3 billion increase for the lunar return effort garnered headlines, the PBR touches every program within NASA’s expansive portfolio, including planetary science, an area of particular interest to The Planetary Society.

Overall, NASA’s Planetary Science Division fares well in the FY 2021 budget request, with a few significant caveats. The promised start of a planetary defense mission to find and characterize hazardous near-Earth objects failed to materialize in the proposal. And 2 productive Mars missions—Mars Science Laboratory (Curiosity) and Mars Odyssey—face steep cuts that would dramatically reduce the quantity and quality of science data returned by the rover and functionally end the Odyssey mission.

The Mars Science Laboratory is the Curiosity rover. Landing on Mars on August 6, 2012, it has been exploring continuously since, and carries, according to its Wikipedia page, 14 instruments.

Mars Odyssey is a Martian orbiter that reached Mars and achieved orbit on October 24, 2001; at nearly 19 years of service, it is the oldest Martian vessel. It studies Mars for water resources, its radiation environment, and its geology. At least one of its experiments has terminated due to damage from the environment.

Here’s the thing. Sure, these are older missions. However, getting to Mars is a chancy business, so when a mission successfully reaches the target, it should be leveraged for every bit of scientific data that can be wrung out of it before the harsh environment knocks it down.

In other words, this is an investment. If the current Administration is going to characterize itself as being run by businessmen, well, they’d better try to pretend they know what that means. Throwing away a beach head that cannot be easily reacquired once our forces have left, if I may employ a military metaphor, isn’t what a good businessman does.

Yeah, it’s great that other research areas are getting increased funding, but how about these missions that are already there and are cheap to run? That’s economizing, even if you have to increase the NASA budget to cover those other targets, politically motivated or not.

This won’t become a political football – NASA’s not that important to the American future or psyche in the current political climate. But it does symbolize the foolishness that pervades this Administration.

A new poll is out suggesting incumbent Senator Martha McSally (R-AZ) is losing traction to challenger, former astronaut, and husband to former Rep Gabby Gifford (D-AZ) Mark Kelly (R-AZ).

Arizona’s Electoral College votes could be in play in November, according to a Monmouth (“Mon‐muth”) University Poll of registered voters in the state. Joe Biden has a slight lead over President Donald Trump, while Bernie Sanders is basically tied with the incumbent. In tomorrow’s Democratic primary election, Biden has a 20 point lead over Sanders. The poll also finds that the Arizona U.S. Senate race could start off with a Democratic edge as well, with Mark Kelly having a 6 point lead against Martha McSally. [Monmouth University Poll]

For a state which acquired a ferocious reputation in 2016 when a traditionally Republican paper endorsed Clinton and was bombarded by hate mail, I’m fascinated to see Biden has a lead over Trump, as well as Arizona’s other Senate seat now being in danger. Remember, McSally ran for, and lost, the seat now held by Kyrsten Sinema (D-AZ); she only occupies the other seat due to an appointment by Governor Doug Ducey (R-AZ). Kelly, whatever his policy proposals, is both an automatic hero and seems like an easily approachable and affable candidate. It’s my guess that he’ll win, possibly by as many as five points – and McSally will be washed up. A result that wouldn’t bother me, given her disrespect for the press.

In 2016, the state went for Trump by less than 4 points. Could the eleven Arizona Electoral Votes be in play? There are still a number of months to go before the Election of the Geriatrics takes place, but this may be worrisome for Republican officials. If government efforts to ameliorate the effects of the Covid-19 pandemic are ineffective, Trump may begin losing the elderly conservative vote. People don’t like losing their friends to something that didn’t have to be as bad as it might be.

But let’s hope it doesn’t go that far.

Suing some dude pretending to be an insulting cow on Twitter should disqualify the litigant from serious consideration of anything, much less holding public office and dispensing advice to the citizens of the nation – and, yet, Rep Devin Nunes (R-CA) just keeps on being a nutcase:

Republican Rep. Devin Nunes of California on Sunday contradicted health experts’ recommendation that Americans practice “social distancing” to curb the spread of coronavirus, instead urging “healthy” Americans to continue patronizing businesses during the pandemic.

“If you’re healthy, you and your family, it’s a great time to go out and go to a local restaurant, likely you can get in easily,” Nunes said during an interview on Fox News as many cities announced new restrictions on bars and restaurants to limit gatherings.

“Let’s not hurt the working people in this country … go to your local pub,” he added.

The suggestion directly contradicts recommendations put forth in recent days by government agencies and public health experts. The Centers for Disease Control and Prevention has been urging “social distancing” — defined as “remaining out of places where people meet or gather” and “avoiding local public transportation” — even if you don’t have any symptoms of the virus as a way to slow the spread of the disease. [CNN]

Sheesh. Why does the 22nd District of California keep reelecting this clown? Is this guy a medical professional with a concentration in public health? No, he’s an Ag guy.

Typical amateur behavior: thinking you know more than folks who’ve somberly studied the problem for years. I hope he takes his broken-down car to a ten year old for repairs. Practice what you preach, Rep Nunes, eh?

Embargo Watch has been around for a decade and more. From author Ivan Oransky’s first post way back when:

If you’re unfamiliar with embargoes: You’ve probably noticed that every major news organization — including mine, Reuters  — seems to publish stories on particular studies all at once. Embargoes are why.

A lot of journals, using services such as Eurekalert.org, release material to journalists before it’s officially published. Reporters agree not to publish anything based on those studies until that date, and in return they get more time to read the studies and obtain comments.

That would seem to be a good thing for science and health journalism, much of which is reliant on journals for news because it’s peer-reviewed — in other words, it’s not just a researcher shouting from a mountaintop — and punctuates the scientific process with “news events.”

Vincent Kiernan doesn’t agree. In his book, Embargoed Science, Kiernan argues that embargoes make journalists lazy, always chasing that week’s big studies. They become addicted to the journal hit, afraid to divert their attention to more original and enterprising reporting because their editors will give them grief for not covering that study everyone else seems to have covered.

But even if embargoes are a necessary evil, they’re not uniform, and how each organization deals with them provides case studies in some of the chinks in embargoes’ armor.

As a fan of obscure facts, it’s interesting to see what other people think is worth blogging about.

Benjamin Wittes of Lawfare has little patience for President Trump’s antics, especially when it comes to important pieces of legislation related to surveillance:

President Trump took a brief break from his busy schedule of bungling the federal response to coronavirus and modeling disasterous presidential leadership in a crisis to, once again, make a fool of his attorney general.

At 10:44 am on March 12, with the Dow Jones having shed nearly 2,000 points since the markets had opened, the president tweeted:

Many Republican Senators want me to Veto the FISA Bill until we find out what led to, and happened with, the illegal attempted “coup” of the duly elected President of the United States, and others!

— Donald J. Trump (@realDonaldTrump) March 12, 2020

Trump did not mention Attorney General Bill Barr in issuing this veto threat concerning the bipartisan compromise bill to reauthorize expiring FISA authorities. He didn’t need to. The day before, on behalf of the Trump administration, Barr had issued a statement that described the bill as follows: …

Where AG Barr states that he’s been working carefully with Congress on the issue and approves the result. See the link if you enjoy careful lawyer talk, but that is what it says.

This is all about keeping the base all stirred up about an alleged witch hunt. Keep shouting out the lie, deny the Mueller report found anything, keep attention focused on some minor issues which may have needed correction, but were, by the government’s own admission, not disqualifying of the actual Page investigation. It’s all about outrage and victimization.

And that’s not how to run a government.

Over on Stratecherry Ben Thompson discusses a number of technical aspects of SARS-CoV-2 and the disease it’s causing, COVID-19. Among other things, he gets into a bit of information composition theory, which is a some jargon I just made up:

The Internet, though, threatens second estate gatekeepers by giving anyone the power to publish:

Just as important, though, particularly in terms of the impact on society, is the drastic reduction in fixed costs. Not only can existing publishers reach anyone, anyone can become a publisher. Moreover, they don’t even need a publication: social media gives everyone the means to broadcast to the entire world. Read again Zuckerberg’s description of the Fifth Estate:

People having the power to express themselves at scale is a new kind of force in the world — a Fifth Estate alongside the other power structures of society. People no longer have to rely on traditional gatekeepers in politics or media to make their voices heard, and that has important consequences.

It is difficult to overstate how much of an understatement that is. I just recounted how the printing press effectively overthrew the First Estate, leading to the establishment of nation-states and the creation and empowerment of a new nobility. The implication of overthrowing the Second Estate, via the empowerment of commoners, is almost too radical to imagine. [From an earlier post by Thompson -HAW]

The current gatekeepers are sure it is a disaster, especially “misinformation.” Everything from Macedonian teenagers to Russian intelligence to determined partisans and politicians are held up as existential threats, and it’s not hard to see why: the current media model is predicated on being the primary source of information, and if there is false information, surely the public is in danger of being misinformed?

The Implication of More Information

The problem, of course, is that focusing on misinformation — which to be clear, absolutely exists — is to overlook the other part of the “everyone is a publisher” equation: there has been an explosion in the amount of information available, true or not. Suppose that all published information followed a normal distribution (I am using a normal distribution for illustrative purposes only, not claiming it is accurate; obviously in sheer volume, given the ease with which it is generated, there is more misinformation):

And then Thompson gets on to discussing how he thinks true and false information fill out the area under the bell curve – see right. What impressed me, however, was his omission of perhaps the most important part of any diagram of this sort – the absorption rate of consumers of this information.

Look, in computer science we often talk about data sources and data sinks. The former term should be self-explanatory, but it means the source of the data to be processed: files on disks, data coming from a network link, etc. A data sink, on the other hand, is the processor of that data: how it’s analyzed, transformed, and stored (each of those steps may be omitted, depending on requirements)^[1].

Now, what happens if your data source is providing data faster than your data sink can process it? It’s a complex problem which, depending on the requirements again, can result in queueing data on disk to just throwing away data on a random basis.

In either of the above diagrams, it would be very helpful to have an estimate of the data processing capability of an individual. Long time readers of this blog know that I have a minor fascination with bell curves (and maybe that’s why I’m driven to comment on Thompson’s post), but in this case I don’t see data processing having a bell curve.

Rather, I think the naive supposition would be that it’s a straight horizontal line. Our capacity to process doesn’t increase just because there’s more information out there.

But, worse yet, it may actually decrease, depending on what you’re measuring. True, a simple definition won’t yield much change, but what if you change it to primary information absorbed? I suggest that distraction by the increasing volume of information, since we’re not single-minded computers^[2], would actually decrease our ability to absorb information. Call the loss absorption of meta-data, if you like. I have experienced this myself as I’ve found long-form journalism sometimes difficult to process when I know I can get scatter-shot tidbits off of Facebook and the like.

But, worse yet, for the conscientious, the awareness of false information drives a requirement that we somehow verify the information that is candidates to be processed! That, in itself, takes time and energy from the actual processing – sometimes vast amounts. This changes the net amount of true information that we can absorb.

I think that would have made Thompson’s chart much more interesting.

¹ I’m sure I’ve dropped out a few steps, as my training is from a long time ago and I’m absent-minded, so be nice if you’re going to bust my chops.

² I suppose we could draw an analogy with thread-programming, but why bother? I’m not aware of every single issue with thread programming, as my exposure to it is only in the highly obscure language Mythryl.

Technically, The Pale Horse (2020) is a two part TV series by the BBC, but I’m calling it a movie because that’s how it felt. As a standalone movie, it was nicely done: excellent acting, good cinematography, fun little plot.

At this point, I must admit I’ve never read The Pale Horse, the Agatha Christie novel on which this movie is based, but my general experience with Christie is that she’s a rationalist. She has no problems placing supernatural elements in her books, but by the time the story comes to a close, they have been cleverly explained by one expedient or another. Christie’s interests were not in supernatural horror as a naive element, but as an element of deceit. Ultimately, Christie was interested in people making bad decisions, and what drove them to it.

But the tendency of this movie to explore the dreams of the lead character, Mark Easterbrook, as a major driver of his actions was a little too disturbing, especially in an ending that is entirely too difficult to credit to Christie. It’s true that the movie follows one of her themes, which is the decay of the upper classes of the Great Britain of her times, but it goes off the rails when Easterbrook is either literally sent to his personal Hell – or at least dreams it. It’s quite the jarring ending, no matter how you feel about the rest of it.

But the professionalism of the production was still encouraging and made for an enjoyable – mostly – afternoon view.

Trying to be a proper skeptic and a reader of Skeptical Inquirer, it’s natural for me to wonder at a TCM (Traditional Chinese Medicine) remedy for Covid-19, but others might not. I hadn’t heard of any, much to my surprise, until I ran across this post tonight by Dutch microbiologist and science integrity consultant Elisabeth Bik on Science Integrity Digest via Retraction Watch:

The recent COVID-19 outbreak has led to an enormous amount of preprints and rapidly-approved papers of variable quality. A recently published paper in Pharmacological Research called “Traditional Chinese Medicine for COVID-19 Treatment” caught my eye. The title suggested that Traditional Chinese Medicine (TCM) could be used to treat patients that had fallen ill with the viral disease, but a quick read showed that the paper promised much more than it delivered. Here is a critical review.

The paper starts off with a description of the COVID-19 outbreak and how Traditional Chinese Medicine (TCM) might bring new hope to treat the disease. It describes the successful treatment of a COVID-19 patient with plant-based mixture called qingfei paidu decoction (QPD). At first glance, this might be a welcome alternative treatment for a novel disease that is quickly growing to be a pandemic, and for which there are no good treatments or vaccines available. But with great claims, we need to see great data, and this is where the paper does not deliver at all.

Want more technical information? Visit Bik’s blog post at the link above. The executive summary is that the paper does not use a proper technique for evaluating the medicine under evaluation, is terribly vague when it should be precise, and a few other errors.

Naturally, many people think there’s a lot of money to be made from a cure, although governments from here to Monte Carlo might declare such a cure to be a public good and pay the inventor enough to cover costs – or make them rich, because who knows how governments would operate these days if presented with such a situation.

But what many don’t realize is that there’s a lot of money to be made with fake cures and vaccines. Just like fly-by-night contractors, dishonest medicine vendors will sell you their verified-by-God cure and then disappear, or refuse to return your money – if, in fact, you do survive long enough to file a complaint in court. See this post on disgraced Evangelical preacher Jimmy Baker.

So if you hear of some TCM, complementary, or other less-than-evidence based cure for COVID-19 that doesn’t really have a good stamp of approval from an accepted authority on it, skip it.