Thursday, June 25, 2020

Covid testing in New Jersey: a tale of two websites

Is New Jersey testing asymptomatic people?

**one internet site says

Testing is available to everyone in New Jersey. Anyone who wants a COVID-19 diagnostic test, can now get one at any of the 250+ testing sites across New Jersey.

To help meet this demand, Attorney General Gurbir Grewal along with the Division of Consumer Affairs, has authorized the more than 18,000 licensed pharmacists in New Jersey to administer FDA-approved or authorized COVID-19 tests to their customers.

Moreover, the Division's order allows for these tests to be given without a prescription, and removes the requirement that pharmacists enter into explicit collaborative practice agreements with a physician.

But the Somerset/Hunterdon NJ site at RVCC tells a different story as of Thursday, June 25, Friday June 26, 2020:

New Date Added for COVID-19 Drive-thru Testing
July 2, 2020
Post Date:06/19/2020 2:32 PM

BRANCHBURG – Somerset County is announcing an additional date of Thursday, July 2, for COVID-19 drive-thru testing at Raritan Valley Community College [RVCC]. Reservations for June 25 have been filled, but spaces are currently available on the first Thursday in July.

Testing, which is free of charge, is open to Hunterdon and Somerset County residents, age five (5) and older, who are exhibiting symptoms. Residents must have a valid doctor’s prescription, ID and an appointment to receive testing.

Appointments for July 2 can be scheduled online at Residents who do not have computer access or who would like to schedule an appointment for children age five to 18 years old can call the COVID-19 testing information line at 908-237-7150, Monday through Friday, from 9 a.m. to 1 p.m.

Patients are required to provide a copy of their prescription, either by bringing it with them to the testing site, or by sending a copy in advance. Prescriptions can be sent via email to, with the word “Prescription” in the subject line, or faxed to 908-704-8042.

For the safety, health and security of staff and volunteers, patients must arrive by car. The testing site will not allow entry if residents don’t arrive in a vehicle, even if they have a valid driver’s license and prescription. When coming to the testing center, residents are asked to use the main entrance to the college campus, off of Route 28.

Anyone who does not have an appointment and a valid prescription or written order from their physician will be turned away.

Sunday, June 21, 2020

Chuck Todd flunks history 101

On Sunday, 21 June 2020, 0n Meet the Press, Chuck Todd said of Juneteenth:

Alright, let me pause it here. When we come back, there were events across the country this weekend marking Juneteenth, which celebrates the end of slavery in the United States. Up next, why those celebrations may be even bigger next year, and beyond.

[CHUCK TODD resumes:]

Welcome back. Data download time. For many Americans, June 19th, Juneteenth, has long held a special meaning. But for others, especially many white Americans, this was the year it was suddenly recognized everywhere. Even so, momentum to recognize the holiday has actually been building for quite some time. First, let's talk about what it is. Juneteenth commemorates June 19th, 1865. It is the day that Union troops arrived in Galveston, Texas to announce the Civil War was over. The news hadn't reached Galveston yet. And to inform people that the Emancipation Proclamation had freed all enslaved people nationwide. It was more than 100 years later that Texas made Juneteenth an official holiday. And since then, 46 other states and the District of Columbia have joined Texas and done the same, with most doing so since the year 2000.

On 19 June 1865, Major General Gordon Granger announced the Emancipation Proclamation at Galveston, Texas, formally declaring the end of slavery in Texas. Slavery in the United States, especially as to Kentucky and Delaware, would not end until December 1865, with the adoption of the 13th Amendment.

Earlier, on May 13, 1865, the last land battle of the war was fought at Palmito Ranch, near Brownsville, Texas. Some of the Union troops were African Americans, who were well aware of the Emancipation Proclamation and of the surrender of General Lee.

On June 2, 1865, General Edmund Kirby Smith surrendered the Department of the Trans-Mississippi to Major General Edward Canby at Galveston, Texas. The citizens of Galveston were well aware of the status of the war more than two weeks before Granger's proclamation.

It was not until August 20, 1866, more than one year AFTER June 19, 1865, that President Andrew Johnson declared the insurrection officially over and peace restored.

Chuck Todd's "data download" is not only erroneous (slavery in the United States did not end until December 1865 and the Civil War was not deemed over in June 1865) and missing in key details (people in Texas generally and Galveston in particular knew of the status of the war, and of the Emancipation Proclamation before June 19, 1865).

Kirby Smith, who would be the last living full General of the Confederacy (Lee was only number 3 in rank) apparently believed Lee and Johnston had been imprisoned, and would exit to Mexico to avoid being tried for treason.

Governor Cuomo on CBS Sunday Morning on June 21, 2020

Back on June 13, Governor Cuomo of New York quoted numbers created by Instagram people defining an Rt parameter to state that New York had done the best job in the nation controlling Covid19. New Jersey was second best. Hawaii weighed in at 0.99.

In the interview which aired on June 21 on CBS Sunday Morning, Governor Cuomo obliquely referred to the same Instagram numbers. However, on June 21, ten states had lower values of Rt than that of New York. Hawaii, which was below 1.0 on June 13, became the worst state in the nation at an Rt of 1.47, topping that of the second worst state, Florida, which had 1.35.

The website for the Rt numbers is , and notes:

While we make a best effort to accurately describe Rt, nothing can do that perfectly. Please calibrate with other sources, like, as well.

If the Rt parameter is truly "predictive," one wonders why there are such dramatic swings.

link to CBS interview, at 9:44 minutes, the longest segment on CBS Sunday Morning on June 21, 2020:

The moment of nature on CBS Sunday Morning on June 21 was great horned owls at Lake Erie.

Monday, June 15, 2020

With a low Rt, will New York quarantine out-of-staters entering New York??

After New York Governor Cuomo's briefing on June 12, 2020, which included text

Rate of Transmission [Rt[ of .77 Lowest Out of All 50 States


So we are the exact opposite. We, since we've reopened, the number has continued to go down, believe it or not. We reopened. It continues to go down because we've been disciplined in our reopening, and that's what we have to continue to do. This is a website where the founders of Instagram now track the rate of transmission of states across the nation. New York State, the lowest rate of transmission, meaning the virus is spreading at the lowest rate in the State of New York, of every state in America, that is incredible. We were the number one state in terms of infection, number one in the nation, number one on the globe per capita, and now we're the last state in terms of rate of transmission. That is because New Yorkers stepped up, they were smart, they were disciplined, they did what they had to do, and we have to stay there. We have to stay there. Now is no time to forget what got us here. We have to stay smart.


I joked to a friend that the next thing that would happen would be an attempt by New York to quarantine out of state people coming INTO New York.

Well, one only had to wait till Monday, June 15. The CBS880 link paraphrases Cuomo's remark as

The governor says a primary concern right now is contagion coming from outsiders who are visiting New York.


The actual audio is a bit more interesting.

****Separately, some background on Ro

From wikipedia:

During an epidemic, typically the number of diagnosed infections N(t) over time t is known. In the early stages of an epidemic, growth is exponential, with a logarithmic growth rate[citation needed]

{\displaystyle K={\frac {d\ln(N)}{dt}}.}
For exponential growth, N can be interpreted as the cumulative number of diagnoses (including individuals who have recovered) or the present number of diagnosed patients; the logarithmic growth rate is the same for either definition. In order to estimate R_{0}, assumptions are necessary about the time delay between infection and diagnosis and the time between infection and starting to be infectious.

In exponential growth, K is related to the doubling time T_{d} as

{\displaystyle K={\frac {\ln(2)}{T_{d}}}}.
Simple model[edit]
If an individual, after getting infected, infects exactly R_{0} new individuals only after exactly a time \tau (the serial interval) has passed, then the number of infectious individuals over time grows as

{\displaystyle n_{E}(t)=n_{E}(0)\,R_{0}^{t/\tau }}

{\displaystyle log(n_{E}(t))=log(n_{E}(0))+log(R_{0})t/\tau .}
In this case,

{\displaystyle R_{0}=e^{K\tau }} or {\displaystyle K={\frac {\ln R_{0}}{\tau }}}.
For example, with {\displaystyle \tau =5~\mathrm {d} } and {\displaystyle K=0.183~\mathrm {d} ^{-1}}, we would find {\displaystyle R_{0}=2.5}.


Definitions from article by Y. Ma (2018) [
Epidemiol Infect. 2018 Sep; 146(12): 1478–1494.
Published online 2018 Jul 4. doi: 10.1017/S0950268818001760

The reproductive number and serial interval (SI) are two key quantities in describing transmission of an infectious disease. The reproductive number is defined as the average number of secondary cases a primary infectious case will produce. In a totally susceptible population, it is referred to as the basic reproductive number (R0); it is referred to as the effective reproductive number (Re) if the population includes both susceptible and non-susceptible persons [6]. An Re greater than 1 indicates that the disease will continue to spread while an Re less than 1 indicates that the disease will eventually die out. Although the reproductive number is usually defined as the average number of secondary cases, it is occasionally defined as the average number of secondary infections [7–10], a distinction that is important for a disease with a long incubation period (the time between infection and developing symptomatic disease) and/or only a fraction of infections progressing to disease. Depending on the setting, the reproductive number can be expressed as a function of parameters such as infection rate, contact rate, recovery rate, making it useful in determining whether or not a disease can spread through a population.

The serial interval (SI), defined as the time between disease symptom onset of a case and that of its infector [11], is a surrogate for the generation interval— an unobservable quantity defined as the time between the infection of a case and the time of infection of its infector [12]. The SI is an important quantity in the interpretation of infectious disease surveillance data, in the identification of outbreaks, and in the optimization of quarantine and contact tracing.

[lbe note: the serial interval is the time between when the infector shows symptoms and the infectee shows symptoms. If asymptomatic people can infect others, one immediately sees a problem here. R becomes undefined if tau becomes undefined.]

***As to covid19, one would have to estimate serial interval from information OUTSIDE OF new cases/per day, but this could be done and such number would be expected to be a known number with a range of uncertainty.
However, R is not knowable from new cases per day or from any data available. In fact, in the tb case, one creates models and chooses R based on a "best fit." From Ma on tb:

Three articles used either approximate Bayesian or exact likelihood methods, 24 articles used either a mathematical model fit with empirical data or a descriptive/regression approach on empirical data, and 29 articles used a simulation based mathematical model

Parameters involved in Covid19 forecasts

**New York Governor Cuomo said:

So we are the exact opposite. We, since we've reopened, the number has continued to go down, believe it or not. We reopened. It continues to go down because we've been disciplined in our reopening, and that's what we have to continue to do. This is a website where the founders of Instagram now track the rate of transmission of states across the nation. New York State, the lowest rate of transmission, meaning the virus is spreading at the lowest rate in the State of New York, of every state in America, that is incredible.



These are up-to-date values for Rt, a key measure of how fast the virus is growing. It’s the average number of people who become infected by an infectious person. If Rt is above 1.0, the virus will spread quickly. When Rt is below 1.0, the virus will stop spreading.

The metric being tracked here (Rt) represents the effective reproduction rate of the virus calculated for each locale. It lets us estimate how many secondary infections are likely to occur from a single infection in a specific area. Values over 1.0 mean we should expect more cases in that area, values under 1.0 mean we should expect fewer

The new version of this model accounts for variation in serial interval and delay between onset of symptoms and a positive test. Because of these changes, it is also more robust to large changes in reported tests. However, this also means that Rt will be far less variable day-to-day than the previous model. [This sounds like Ro.]

There is an incubation period in which people are likely infectious but not symptomatic. This model assumes infectiousness begins with symptoms. While future versions may correct for this, a simple heuristic is to shift all values of Rt 5 days into the past.
While we make a best effort to accurately describe Rt, nothing can do that perfectly.


One cannot be sure "how qualified" the people at Instagram are to assess Rt, which does sound like Ro. Their Rt is clearly NOT a rate; it is dimensionless. If you believe this stuff, you should be worried, because Hawaii is at 0.99, not like a safe state like NY or NJ, which are the two "best" states (lowest Rt)

As usual, the data relied upon is tests of symptomatic people. Although they make a nod to pre-symptomatic people, they ignore asymptomatic people (who never get symptoms). If one is worried about the kinetics of spreading, this is incomplete, because it ignores: asymptomatic to symptomatic, symptomatic to asymptomatic and asymptomatic to asymptomatic.

At this point in time, this is not a viable approach.

Recent work by Aravinda de Silva of UNC shows how we can fine tune analysis of "asymptomatic" individuals.

From Genetic and Engineering News:

The antibody test is based on the receptor-binding domain (RBD) of the spike protein. The RBD-based antibody test measures the levels of that domain, which the authors found correlate to the levels of neutralizing antibodies related to the paper published in Science Immunology titled “The receptor-binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients.”

[The importance resides in specificity to Covid19]

The RBD of the spike protein in SARS-CoV-2 is not shared among other known human or animal coronaviruses. Therefore, antibodies against this domain are likely to be highly specific to SARS-CoV-2, and so these antibodies reveal if an individual has been exposed to the virus that can cause COVID-19.

[Of data]

By day 9 after the onset of symptoms, the authors wrote that “the recombinant SARS-CoV-2 RBD antigen was highly sensitive (98%) and specific (100%) for antibodies induced by SARS-CoVs.” They noted that they observed a strong correlation “between levels of RBD binding antibodies and SARS-CoV-2 neutralizing antibodies in patients.”

[Of the relevance to asymptomatic people]

“We don’t see our research as a means to replace commercial tests,” said de Silva. “Commercial tests are critical, especially for making decisions about the clinical management of individual patients. But it’s too early in the pandemic to know if the commercial assays are suitable for identifying people who experienced very mild or no disease after infection or if the assays tell us anything about protective immunity, as researchers are still learning about this virus.”

Did Jefferson Davis commit treason?

The Guardian discussed Jefferson Davis on 13 June 2020:

The Confederacy lost the war and slavery was abolished under the 13th amendment, ratified in December 1865. Davis was charged with treason but never tried, having his citizenship stripped instead. He died in New Orleans in 1889.


Jefferson Davis was indicted by a grand jury convened by federal district court judge John Underwood. From there, the story gets complicated, related in part to presidential ambitions of Salmon Chase (then Chief Justice of the Supreme Court) and the overlapping-in-time impeachment of Andrew Johnson.

At the time of the indictment, federal high crimes (such as treason) had to be overseen by the district judge in the jurisdiction of the crime (here Virginia, the location of Judge Underwood) and the relevant Supreme Court Justice (here, Salmon Chase, who oversaw the Fourth Circuit). Chase could foretell that the case would involve the legality of secession. Jefferson Davis would argue Davis did not commit treason, because he was no longer a citizen of the United States. If secession were constitutional, this might be a valid defense. Chase himself had states rights leanings, even though he was an abolitionist. Of all people, Thaddeus Stevens offered to defend Davis, because Stevens wanted the Confederacy to be viewed as a conquered nation, under complete military control.

The impeachment proceedings against Johnson kept delaying Davis' trial. Horace Greeley and Cornelius Vanderbilt helped to obtain bail for Davis.
Chase ruled that section 3 of the 14th Amendment, which gave limitations of rights on former Confederate officials, defined the ONLY limitations which could be imposed. Thus, effectively, the indictment for treason was unconstitutional. Johnson pardoned Davis before the full Supreme Court could rule on treason by Davis.

Ironically, both Chase and Johnson were considering running as Democrats in the 1872 election. Johnson, after all, was a Democrat, and Chase was shifting.

Some relevant links:

Washington Post, In 1868, the fate of Jefferson Davis’s neck swung on Andrew Johnson’s impeachment, Ronald G. Shafer
Feb. 2, 2020 at 7:00 a.m. EST

**Some have argued that the federal government, in referring to its naval action against the Confederacy as a blockade (as distinct from a port closing) admitted that the Confederacy was a sovereign government

Sunday, June 14, 2020

On the meaning of "Juneteenth"

One commenter on the Trump/Juneteenth/Carson matter wrote the following:

Carson...was "pleasantly surprised" by how much Trump knew about Juneteenth, which commemorates the end of slavery in the United States."

He was surprised Trump knew anything at all. Note how Carson didn't detail what Trump knew about it.

June 19 became "Juneteenth" because on June 19, 1865, Union major general Gordon Granger informed residents of Galveston, Texas that slaves in Texas were free by virtue of the Emancipation Proclamation, which had taken effect, in Texas, on January 1, 1863. The state of Texas, one of eleven states of the Confederacy, was the last Confederate state to fall, at least nominally, under control of Union forces, and thus ended slavery in the Confederate states, although not exactly by virtue of the Emancipation Proclamation.

The above commenter is wrong because Juneteenth does not mark the end of slavery in the United States.

Henry Louis Gates, Jr. wrote

The Emancipation Proclamation itself, ending slavery in the Confederacy (at least on paper), had taken effect two-and-a-half years before [Juneteenth], and in the interim, close to 200,000 black men had enlisted


But even this is not correct. The Emancipation Proclamation mentions only ten of the eleven Confederate states, pointedly omitting the state of Tennessee. The Emancipation Proclamation did not end slavery in Tennessee. Separately, the Emancipation Proclamation also excluded certain parts of Louisiana and Virginia. Further, the Emancipation Proclamation did not end slavery in the border (slave) states of Missouri, Kentucky Maryland, and Delaware. [There was alavery in New Jersey, but that is a different story.]

By the time of Juneteenth 1865, slavery had been eliminated by state action in Missouri, Maryland, and Tennessee.

However, this technicality does not absolve the commentator (or others who believe the Juneteenth celebrates the end of slavery) because slavery did not end in Kentucky and Delaware until the adoption of the Thirteenth Amendment on December 18, 1865.

In fact, Delaware did not ratify the the 13th Amendment until 1901; Kentucky until 1976. Of interest, one notes both Civil War presidents, Lincoln and Davis, came from Kentucky.

In passing, one notes that the following map from


is in error: