Gaining depth on gain of function

(Scott Johnson)

Yesterday I posted “The fallacious Fauci strikes again.” My comments elicited a message from Michael S. Rogers, Assistant Professor of Surgery at Harvard Medical School and Research Associate in the Vascular Biology Program at Boston Children’s Hospital. I thought some readers might find it of interest. With his permission I am posting his message below the break.

 

Source: Gaining depth on gain of function

MIT Study: Vaccine Hesitancy Is ‘Highly Informed, Scientifically Literate,’ and ‘Sophisticated’

Sometimes the perception of irrationality is almost accidental, because arguments are usually social interactions, not strictly logical exercises. A vaccine skeptic may brush off a proponent by saying, “It’s approved for emergency use only; it’s not FDA-approved. I don’t think we should require it.” The skeptic is beginning with a fact that’s easily established and shareable. But when pressed, they might reveal that their line of thinking is elsewhere: “There are no long-term studies, and I’m worried about possible long-term effects.” Because the two objections aren’t exactly logically connected, the proponent concludes it is irrationalism all the way down.

But a study done at MIT showed that a substantial portion of public-health skepticism was highly informed, scientifically literate, and sophisticated in the use of data. Skeptics used the same data sets as those with the orthodox views on public health.

Source: MIT Study: Vaccine Hesitancy Is ‘Highly Informed, Scientifically Literate,’ and ‘Sophisticated’

The most recent Kaiser poll helps illustrate that the vaccine hesitant group doesn’t really lean Republican. Just 20% of the group called themselves Republican with an additional 19% being independents who leaned Republican. The clear majority (61%) were not Republicans (41% said they were Democrats or Democratic leaning independents and 20% were either pure independents or undesignated).

CNN

Putting the Biden government’s COVID pressure in a proper historical context

With a historical perspective, it’s plain that Fauci, Facebook, and Biden are being hysterical about vaccines solely to increase their power. On Friday, Pervy Joe, the man occupying the White House, insisted that Facebook was “killing people” because it wasn’t censoring enough information about COVID.

Source: Putting the Biden government’s COVID pressure in a proper historical context

I THINK I KNOW THE ANSWER: Are Activists Protecting Asians from Hate–Or Protecting Their Narrative …

I THINK I KNOW THE ANSWER: Are Activists Protecting Asians from Hate–Or Protecting Their Narrative of White Supremacy from Criticism?

Source: I THINK I KNOW THE ANSWER: Are Activists Protecting Asians from Hate–Or Protecting Their Narrative …

Asia Society, the global NGO dedicated to “forging closer ties between Asia and the West through arts, education, policy and business,” recently shared a video in which activist Manjusha P. Kulkarni spoke about anti-Asian attacks in the United States. Kulkarni, whose own group self-describes as a “national coalition addressing anti-Asian hate amid the COVID-19 pandemic,” emphasised that anti-black bigotry was causing people to falsely attribute these anti-Asian attacks to African American perpetrators:

And I will tell you that while we don’t collect ethnic specific data on perpetrators … we know that it is a very small minority that are African-American. And in fact, when we look at these broader types of discrimination, the ones that involve civil-rights violations, of course, we know that those are institutional actors, heads of businesses, et cetera, and that these are the folks who often, because of positions of power that they are in, are actually white.

The United States has witnessed some truly shocking anti-Asian attacks in recent months. On January 28th, 84-year-old Vicha Ratanapakdee was out for a walk in San Francisco when he was violently shoved to the ground. He never regained consciousness after the assault. On January 31, in Oakland, a 91-year-old Asian man was shoved from behind, unprovoked. The same assailant later pushed a 60-year-old man and a 55-year-old woman to the ground, resulting in the woman losing consciousness. In March, an Asian woman in Bronx was struck on the head with an umbrella by four teenage girls who accused her of spreading COVID-19. On March 21st, in Manhattan, a woman was on her way to an anti-Asian violence protest when a man tore up her sign, and hit her twice in the face. During the same month, also in Manhattan, an Asian woman was knocked to the ground and kicked when she was on her way to church—footage shows some security guards looking on and doing nothing. On April 23rd, a 61-year-old Asian man in New York was struck in the back and knocked down; the suspect then stomped on his head repeatedly. On May 2nd, two Asian women were walking on the sidewalk in New York when an individual demanded they remove their masks and then struck one of the women on the head with a hammer. On May 4th, 85-year-old Chui Fong Eng and another woman were stabbed in broad daylight in San Francisco while they waited for a bus; Eng was left with a blade in her torso, which had to be removed surgically. Also in May, a 36-year-old Asian man was pushing his baby in a stroller outside a San Francisco supermarket when he was attacked; footage shows that he was trying to block blows to the head and back as his stroller rolled away.

If you have been following the news about such anti-Asian attacks in the United States over the past few months, you may have noticed that certain narratives have become prominent. The first—promoted by CNNthe GuardianNPRBBCUSA Todaythe Cut, and NBC News, to name just a few representative examples—is that the attacks are related to COVID-19. And it is true that there has been a rise in hate crimes against Asian Americans during the pandemic. In some cases, the attackers have even made explicit mention of the “Chinese virus,” or accused the victim of bringing the disease to the United States. In most cases, however, it is difficult to prove that any given attack is related to the pandemic.

A second theme has been the idea that Donald Trump is to blame for anti-Asian hate. Examples here include “‘No question’ Trump’s racist rhetoric fuelled anti-Asian hate, says White House” (the Independent), “Trump’s ‘Chinese Virus’ Tweet Helped Fuel Anti-Asian Hate On Twitter, Study Finds” (Forbes), and “U.S. outrage over Donald Trump’s racist rhetoric took a new turn this week after shootings at spas near Atlanta” (ABC News).

It certainly wasn’t helpful for the then-US president to describe COVID-19 as “Chinese virus” and “Kung Flu,” especially when there are so many people who cannot seem to understand the distinction between the Chinese government and Asian Americans. There also seems to be a link between his expressions of bigotry and the appearance of copycat anti-Asian memes online. However, it was not until the beginning of 2021—nearly a year after the pandemic began, and a time when Trump was already out of office—when the surge in senseless attacks on Asian Americans began to be widely reported. The timing here is not consistent with the idea that Trump played a major role.

A third media narrative has been that anti-Asian violence is caused by white supremacy. At CNN, the headline was “White supremacy and hate are haunting Asian Americans.” At the State Press in Arizona, “Anti-Asian racism is a product of white supremacist norms that must be eliminated.” At the Conversation, “White supremacy is the root of all race-related violence in the US.”

Paradoxically, the backdrop to these articles is that in many cases—including every one of the examples I mentioned earlier in this essay—the suspects were found to be black. Explaining why black attacks on Asian victims is really the fault of white supremacy may seem difficult, but a surprisingly large number of writers and scholars have shown themselves eager to take up the challenge.

….

This brings us to the issue of crime statistics. Pandika bases her claims on a University of Michigan Virulent Hate Project study of news articles that describe incidents of anti-Asian racism. “In the 4,337 news articles that we reviewed, we identified 1,023 unique incidents of anti-Asian racism that occurred in the United States between January 1 and December 31, 2020,” the authors reported. And while “only a small fraction of news articles explicitly identified the race of the individuals who harassed or discriminated against Asian and Asian American people … in the few harassment incidents for which the news media explicitly stated the race of the offender, the majority of perpetrators of anti-Asian harassment were reported to be male and white.”

On page 14 of the study, we learn that the race of offenders was explicitly identified in only 57 anti-Asian harassment incidents. Of these 57 incidents, white individuals were reported as perpetrators in 44, Blacks in six, Hispanics in four, Chinese in three, Vietnamese in one. “The information that we have,” the authors conclude, “while limited and imperfect, does not support the common claim that Black hostility is driving the current epidemic of anti-Asian racism and violence.”

There are a few problems here, however. The first is that the data isn’t comprised of actual crime statistics, but just information gleaned from news articles. And even within those news article, only a tiny minority mention the perpetrator’s race. As the authors themselves note, “reporting practices might differ by the race of the perpetrator, and it is not clear how news outlets and individual reporters chose to navigate the complex issue of racial identification in its coverage of specific incidents discussed in the articles we reviewed.”

….

In regard to actual hate crimes, as that term is defined by the FBI, Voice of America has reported that “only two of the 20 people arrested last year in connection with [New York City anti-Asian hate crime] attacks were white, according to New York Police Department data analyzed by the Center for the Study of Hate and Extremism. Eleven were African Americans, six were white Hispanics and one was a Black Hispanic.” According to the reporter, Masood Farivar, “most police departments do not publish this kind of data, but anecdotal evidence suggests the pattern seen in New York has emerged in other cities, as well.”

Source: Quillette.com

 

Trump Vindicated (Again) by New Study on Hydroxychloroquine

A new study shows that hydroxychloroquine (HCQ), the antimalarial drug, combined with azithromycin (AZM), could increase the rate of survival by nearly three times for severely ill COVID-19 patients. The observation study analyzed 255 mechanically ventilated patients at the Saint Barnabas Medical Center in New Jersey.

“We found that when the cumulative doses of two drugs, HCQ and AZM, were above a certain level, patients had a survival rate 2.9 times the other patients,” the study, published by medRxiv. says in its conclusion.

By using causal analysis and considering of weight-adjusted cumulative dose, we prove the combined therapy, >3 g HCQ and > 1g AZM greatly increases survival in Covid patients on IMV and that HCQ cumulative dose > 80 mg/kg works substantially better. These data do not yet apply to hospitalized patients not on IMV. Since those with higher doses of HCQ had higher doses of AZM, we cannot solely attribute the causal effect to HCQ/AZM combination therapy. However, it is likely AZM does contribute significantly to this increase in survival rate. Since higher dose HCQ/AZM therapy improves survival by nearly 200% in this population, the safety data are moot.

An analysis of hospitalized COVID patients from last year in New York State’s largest health system found that the death rate of COVID-19 patients on mechanical ventilation was 88 percent, compared to 21 percent overall, when treated with the HCQ/AZM combination.

….

There have now been over 250 studies into hydroxychloroquine’s effectiveness in treating COVID-19, the overwhelming majority of them showing positive results. Studies on early treatment with the drug showed a 66% improvement in mortality rates. But the media chose to ignore those studies, instead deciding to report on a few heavily flawed studies that allegedly showed the drug was either ineffective or increased mortality.

Dr. Fauci also dismissed the drug’s potential for treating COVID patients, claiming that “valid” scientific data showed hydroxychloroquine wasn’t effective in treating COVID-19.

Last year, as data continued to show that hydroxychloroquine was actually effective in treating COVID-19, doctors who spoke out in support of the drug were censored.

And the human cost of this media assault on hydroxychloroquine was catastrophic. One analysis suggests that over 2.4 million lives worldwide have been unnecessarily lost because hydroxychloroquine was not being widely used as a COVID therapeutic. That’s a lot of people who may have died unnecessarily just because the media hated Trump.

Source: Trump Vindicated (Again) by New Study on Hydroxychloroquine

Why the Science Points to a Lab Leak

In today’s Wall Street Journal, two eminent scientists explain why the evidence points toward a laboratory origin for the covid-19 virus:

In gain-of-function research, a microbiologist can increase the lethality of a coronavirus enormously by splicing a special sequence into its genome at a prime location. Doing this leaves no trace of manipulation. But it alters the virus spike protein, rendering it easier for the virus to inject genetic material into the victim cell.
***
In the case of the gain-of-function supercharge, other sequences could have been spliced into this same site. Instead of a CGG-CGG (known as “double CGG”) that tells the protein factory to make two arginine amino acids in a row, you’ll obtain equal lethality by splicing any one of 35 of the other two-word combinations for double arginine. If the insertion takes place naturally, say through recombination, then one of those 35 other sequences is far more likely to appear; CGG is rarely used in the class of coronaviruses that can recombine with CoV-2.

In fact, in the entire class of coronaviruses that includes CoV-2, the CGG-CGG combination has never been found naturally. That means the common method of viruses picking up new skills, called recombination, cannot operate here.
***
Although the double CGG is suppressed naturally, the opposite is true in laboratory work. The insertion sequence of choice is the double CGG. That’s because it is readily available and convenient, and scientists have a great deal of experience inserting it.
***
Now the damning fact. It was this exact sequence that appears in CoV-2. Proponents of zoonotic origin must explain why the novel coronavirus, when it mutated or recombined, happened to pick its least favorite combination, the double CGG. Why did it replicate the choice the lab’s gain-of-function researchers would have made?

Source: Why the Science Points to a Lab Leak

The Lab-Leak Theory: Evidence Beyond a Reasonable Doubt

Every good prosecutor will tell you that the best case is a strong circumstantial case — and that’s exactly what we have.

….

What NR’s Jim Geraghty has chronicled for months is proof beyond a reasonable doubt that the coronavirus pandemic was generated by an accident — a lab leak, a not-uncommon mishap in medical research conducted by fallible human beings — at the Wuhan Institute of Virology. Ditto the important work of Nicholas WadeVanity Fair’s Katherine Eban, our own Michael Brendan Dougherty, and a few intrepid others.

Lab accidents are common, and have been known to spawn infectious diseases (including the escape of SARS1 from the Chinese National Virology Institute in Beijing “no less than four times,” according to Wade). WIV scientists were conducting gain-of-function research on bat-based coronaviruses, in particular their capacity to infect humans. The bats in which are found closely related (but, importantly, not identical) viruses do not inhabit the vicinity of Wuhan — they are nearly a thousand miles away from that densely populated city and have limited flight range. The likelihood of naturally occurring interspecies transmission (outside a lab setting) is infinitesimal. The lab conditions in Wuhan were insufficiently safe — grossly so, it appears. Several of the lab’s researchers fell ill (at least three severely enough to be hospitalized) right at the critical time, in autumn of 2019, before the first identified case of infection with SARS-CoV2, the virus that causes COVID-19.

Here, two additional points are salient. First, those implausibly claiming that the circumstantial case is weak always skip past the inconvenient fact that the circumstantial case for their preferred theory of natural transmission (from bat to human, directly or through an intermediary species) is so weak as to be negligible — there being, most tellingly, no known existence of a bat (or pangolin, etc.) in which a virus matching SARS-CoV2 has been found.

Source: The Lab-Leak Theory: Evidence Beyond a Reasonable Doubt

Over at “Starts With a Bang”, we have a dissenting view:

Despite the enormous scientific knowledge humanity has gained, however, an unfounded conspiracy theory about the virus’s origin has gained a lot of traction: that it was genetically engineered with the purpose of infecting humans, that it was leaked from the Wuhan Institute of Virology, and that’s where it came from. Most recently, disgraced journalist Nicholas Wade has penned an error-filled, misleading piece promoting this nonsense, but the science tells a different story.

Starts With a Bang

Essentially, we don’t have the technology to engineer a virus without lots of human testing, which would have been noticed.

Nothing, though, that I’ve seen disproving the notion that a naturally occurring virus might have been accidentally released from the lab in Wuhan.

Mask mandate and use efficacy in state-level COVID-19 containment

Abstract
Background: Containment of the COVID-19 pandemic requires evidence-based strategies to reduce transmission. Because COVID-19 can spread via respired droplets, many states have mandated mask use in public settings. Randomized control trials have not clearly demonstrated mask efficacy against respiratory viruses, and observational studies conflict on whether mask use predicts lower infection rates. We hypothesized that statewide mask mandates and mask use are associated with lower COVID-19 case growth rates in the United States.
Methods: We calculated total COVID-19 case growth and mask use for the continental United States with data from the Centers for Disease Control and Prevention and Institute for Health Metrics and Evaluation. We estimated post mask mandate case growth in non-mandate states using median issuance dates of neighboring states with mandates. Results: Case growth was not significantly different between mandate and non-mandate states at low or high transmission rates, and surges were equivocal. Mask use predicted lower case growth at low, but not high transmission rates. Growth rates were comparable between states in the first and last mask use quintiles adjusted for normalized total cases early in the pandemic and unadjusted after peak Fall-Winter infections. Mask use did not predict Summer 2020 case growth for non-Northeast states or Fall-Winter 2020 growth for all continental states.
Conclusions: Mask mandates and use are not associated with slower state-level COVID-19 spread during COVID 19 growth surges. Containment requires future research and implementation of existing efficacious strategies.

Medrxiv.org

Shutdowns Were a Disaster [with comment by Paul]

The Wall Street Journal notes that, as the coronavirus disappears in the rear-view mirror, two Americas are emerging:

The unemployment rate in April nationwide was 6.1%, but this obscures giant variations in the states. With some exceptions, those run by Democrats such as California (8.3%) and New York (8.2%) continued to suffer significantly higher unemployment than those led by Republicans such as South Dakota (2.8%) and Montana (3.7%).

It’s rare to see differences that are so stark based on party control in states. But the current partisan differences reflect different policy choices over the length and severity of pandemic lockdowns and now government benefits such as jobless insurance.

Nine of the 10 states with the lowest unemployment rates are led by Republicans. The exception is Wisconsin whose Supreme Court last May invalidated Democratic Gov. Tony Evers’s lockdown. The unemployment rate in Wisconsin is 3.9%—the same as Indiana—compared to 7.1% in Illinois whose Gov. J.B. Pritzker has been slow to reopen.

This chart shows the highest and lowest state unemployment rates:

Of course, blue-state governors who imposed long and stringent shutdowns would say that they did so for reasons of public health. Harsh shutdowns, they may argue, were necessary to slow the spread of the Wuhan virus.

But there is no evidence of any such positive effect. This has been shown over and over in a variety of ways, but let’s add one more. I added up the coronavirus deaths per 100,000 of population, according to the CDC, for the ten states in the Journal’s chart with the highest unemployment rates, and averaged them. I found that the ten states with highest unemployment averaged 202.6 deaths per 100,000. I then did the same thing for the ten states (all but Wisconsin with Republican governors) with the lowest unemployment. Their average deaths per 100,000 was much lower, at 134.5.

PAUL ADDS: ….

A measurement of lockdowns’ adverse effects on unemployment would require a more refined analysis. For example, it seems clear that Hawaii is experiencing the nation’s highest unemployment rate not primarily because it shut down or because it has a Democratic governor, but because it relies so heavily on tourism, and people didn’t want to fly to Hawaii, or couldn’t, during a pandemic (shutdown or not).

….

It’s more probative to compare Minnesota and the Dakotas. Deaths per one million people in Minnesota, where the governor imposed a lockdown, are 1,329. In South Dakota and North Dakota, which did not lock down, deaths per one million are 2,272 and 1,984, respectively (according to numbers reported in Worldometer).

We also know that Sweden, which did not lock down, had vastly more deaths per capita than Norway and Denmark, which did. According to numbers reported in Worldometer, Sweden had 1,419 deaths per one million, compared to 433 in Denmark and only 143 in Norway .

….

JOHN responds: I disagree. Paul doesn’t comment on the Minnesota-Wisconsin comparison, which is as close to apples-to-apples as we are going to get. Minnesota locked down drastically, Wisconsin didn’t, and the coronavirus deaths were identical. As for the Dakotas, North Dakota did lock down, unlike South Dakota, and their death totals are virtually the same.

As I wrote here, an obvious variable is what percentage of a state’s population, pre-covid, was in nursing homes. That percentage varies surprisingly widely from state to state. I looked at the Upper Midwestern states in my post, and found that nursing home population went a long way toward explaining covid death rates. There were many more people in nursing homes, per capita, in Iowa, North Dakota and South Dakota than in Minnesota and Wisconsin before the epidemic began. I also looked at nursing home populations in various states around the country and found similar correlations.

So I continue to believe that there is no sound empirical basis for thinking that lockdowns, or the severity of lockdowns, made a material difference in covid results.

Source: Shutdowns Were a Disaster [with comment by Paul]

COVID and the lab: one of the most consistent things about Trump has been…

…that the vast majority of the things he claimed – and which the press, the left, and the Democrats (but I repeat myself) screamed were preposterous – have turned out to be true.

For example, here’s an interesting tweet to look back on, from over a year ago:

President Trump contradicts the US intel community by claiming he’s seen evidence that the coronavirus originated in a Chinese lab cnn.it/3d7KSuC

The responses are to the effect of “What a liar!” and “What an idiot.”

….

Fast forward to now:

….

Not man-made or modified. The science was settled. Anyone who said otherwise was a wild conspiracy theorist.

Yep. At PolitiFact’s event, advertised as “four days of forward-thinking conversation about the role of facts in our lives,” Dr. Anthony Fauci said he’s not convinced that the virus developed naturally and that “we should continue to investigate what went on in China.”…

Fauci’s comments – given just a few hours after his Senate testimony – were in response to a question from PolitiFact’s Katie Sanders, who asked:

“There’s a lot of cloudiness around the origins of COVID-19 still, so I wanted to ask, are you still confident that it developed naturally?”

Displaying a level of intellectual curiosity heretofore unseen in him by the American public, Fauci replied:

“No, actually. I am not convinced about that. I think we should continue to investigate what went on in China until we continue to find out to the best of our ability what happened.”

Source: COVID and the lab: one of the most consistent things about Trump has been…