NJ 2020 10 31

Above is the doubling time. This is a clear depiction of a second burst compared to early May! However, mortality rates are so low that this appears as a different disease.

 Below is the town and county with the town keeping low but constant and the county with these periodic spikes. I really believe we have massive data reporting problems that have never been fixed.

Town prevalence back up to mid August and even mid May levels. Willing to bet there is some periodic effect occuring, we see this in many osciullatory physican phenomenon and the cause is also the remedy. Don't count on finding it with our wizards in Trenton.

The state is below. Here we are back in April and driven by certain counties.

Morris county shows a peaking again in April. But again very low mortality.

Total mortality has an upward slopw due to numbers.

The short term growth...

Finally mortality shows regrettably the periodic LTC deaths continuing. This is in my opinion criminal.

 

Some Thoughts on Partial Differential Equations

 Now one may suspect that this piece is of little value except to some small band of specialists. I would humbly beg to differ, it is not a discourse on mathematics but on a change in how we are being told to think. Yes, we are being told to accept AI and its great "powers" and take as an answer whatever comes forth. After all these social media platforms use  AI and look how wonderful they have become, NOT.

So the driver was a Technology Review piece, that MIT ersatz related rag that ofttimes yields insight into the minds of the maddening crowd of the social media generation. TR notes:

Unless you’re a physicist or an engineer, there really isn’t much reason for you to know about partial differential equations. I know. After years of poring over them in undergrad while studying mechanical engineering, I’ve never used them since in the real world. But partial differential equations, or PDEs, are also kind of magical. They’re a category of math equations that are really good at describing change over space and time, and thus very handy for describing the physical phenomena in our universe. They can be used to model everything from planetary orbits to plate tectonics to the air turbulence that disturbs a flight, which in turn allows us to do practical things like predict seismic activity and design safe planes. The catch is PDEs are notoriously hard to solve. And here, the meaning of “solve” is perhaps best illustrated by an example. Say you are trying to simulate air turbulence to test a new plane design. There is a known PDE called Navier-Stokes that is used to describe the motion of any fluid. “Solving” Navier-Stokes allows you to take a snapshot of the air’s motion (a.k.a. wind conditions) at any point in time and model how it will continue to move, or how it was moving before.These calculations are highly complex and computationally intensive, which is why disciplines that use a lot of PDEs often rely on supercomputers to do the math.

Then to the rescue comes AI, like a flash, we  get the answer. AI excels where Matlab fails and humans, well we just do not count.

Now I tend to disagree. A good user of PDEs does so by "feeling" the answer, like Luke Skywalker. One can be experienced enough to see the boundary conditions, the infinite time results, the PDEs we have already solved. PDEs are used in Quantum mechanics, heat transfer, electromagnetic theory, and even cancer metastasis. We live in a spatio-temporal world definable in PDEs. 

Take the simple one:

Time rate of change of X = Increase rate of X + Flow rate of X + Diffusion rate of X

Namely this thing X changes by means of it replicating, moving in some flow in and out, and by the random process of diffusing due to bouncing into one another. Most of the world as we know it goes that way. We do not need some large compute with AI to tell us this. We start by understanding if we have captured all the driving effects. Then we measure them again and again. We try to see if each of these effects is linear or some complex non-linear form. We remember the world is always linearizable in the small and this gives us a chance to get a small model. Then back to data gathering. You get it, it is incremental and we are always checking with Mother Nature.

This is the problem with Climate Change. It becomes a massive set of PDEs and we get into a never ending loop of checking.

But, and this is the critical BUT, we often find that our models, and that is what they are, have been delimited by some non-linearity. These factors result in massive changes and make our conclusions suspect. Using AI we may never see these factors, miss these phenomena, and thus diverge to some relatively false solution.

To be successful with PDEs one must live with them. Understand them. They are like predator animals, but after a while you find them like a pet, but still keep it at a distance. Placing it in some AI cage with darkened walls makes this creature foreign and you never really get to know it.

Thus my suggestion, go back to paper and pencil.

Visited Old Tom Today

For those for whom words and actions mean something, not just "ideas", here are the words of Tom Paine, be-smudged across the most sincere part. Paine pleaded with Madison, Hamilton and Washington to rid the new land of the stain of slavery. His very words addressing this point were stained and blotted out above. Words mean something, perhaps folks can re-read Old Tom, I do. Just a note, the Jacobins in the French Revolution had Tom less than a day from beheading. One can always tell the character of a person by that of their enemies, especially those who are unable or refuse to read.

NJ 2020 10 24

 I guess they finally woke up in Trenton so we now have yesterday's stats. Frankly I think they are wrong, LTC is off, but alas what can one expect.

Look at death rate below. Frankly we seem to be at 0.1-0.4% fatality rates, not as grim as was predicted. One suspects that most had some per-existing condition.

The county is coming up slowly due to schools first and gatherings second. All one has to do is see the dozens of school kids walking home and then going into Walgreens to buy candy and effectively spreading it around!

The state is equally reflective of this effect.

Towns still show hot spots.

The town below shows almost periodic outbreaks, not your academic's pandemic model, so much for models!

Here we compare town and county by day and we see clearly the peaking. But as I had noted before there is almost some periodic nature to the reporting. This is why I have said many time the data is truly corrupted!

NJ Stats Update

 Sorry folks but the NJ updater must be asleep. We have just a few counts but we are still waiting. Of course the Gov sent out his response to numbers we cannot see....par for the course....

"Knucklehead" ?

 As nj.com has noted:

Gov. Phil Murphy wasn’t wearing a mask when he came into contact with a senior staffer who has tested positive for the coronavirus Saturday night while they were together at an outdoor area of a Hoboken bar with about a half-dozen others, the governor said Thursday. Murphy, who continues to show no symptoms, left a public event on Wednesday and went into self-quarantine after learning that staffer, Deputy Chief of Staff Mike Delamater, has COVID-19. Murphy took a test that afternoon that was negative, his second negative test this week...

Someone who has been operated on at MSKCC for clear cell renal carcinoma should be a bit more careful especially after enjoining all residents to forego their voting rights to accommodate his demands. Ya think?

To Mask or Not to Mask, That is the Question

 We have been told that masks will prevent us from getting infected. In fact the head of the CDC even told Congress that a mask is better than a vaccine. 

In a September NEJM article the authors state:

One important reason for population-wide facial masking became apparent in March, when reports started to circulate describing the high rates of SARS-CoV-2 viral shedding from the noses and mouths of patients who were presymptomatic or asymptomatic — shedding rates equivalent to those among symptomatic patients. Universal facial masking seemed to be a possible way to prevent transmission from asymptomatic infected people. The Centers for Disease Control and Prevention (CDC) therefore recommended on April 3 that the public wear cloth face coverings in areas with high rates of community transmission — a recommendation that has been unevenly followed across the United States....To test our hypothesis that population-wide masking is one of those strategies, we need further studies comparing the rate of asymptomatic infection in areas with and areas without universal masking. To test the variolation hypothesis, we will need more studies comparing the strength and durability of SARS-CoV-2–specific T-cell immunity between people with asymptomatic infection and those with symptomatic infection, as well as a demonstration of the natural slowing of SARS-CoV-2 spread in areas with a high proportion of asymptomatic infections. Ultimately, combating the pandemic will involve driving down both transmission rates and severity of disease. Increasing evidence suggests that population-wide facial masking might benefit both components of the response.

Now several respondents in NEJM note the opposite:

We caution against incorporating hypotheses about masks functioning as effective “variolation” — a notion that was advanced by Gandhi and Rutherford in the Journal (online September 8) — into public health messaging without considering the implications and nuances. The term “variolation” should be avoided because it is inaccurate with respect to coronaviruses, and it describes an obsolete and risky practice that was used for the iatrogenic inoculation of smallpox. There is insufficient evidence to support the claim that masks reduce the infectious dose of SARS-CoV-2 and the severity of Covid-19, much less that their use can induce protective immunity. Substantial knowledge gaps must be addressed before claims are made about the efficacy of face masks in reducing morbidity or eliciting immune responses. Masks are used primarily to reduce SARS-CoV-2 transmission rather than reduce the dose of infectious particles or mitigate the severity of Covid-19. The suggestion that masks offer an alternative to vaccination without evidence that the benefits outweigh the great risks implicitly encourages reckless behavior. With the lack of a vaccine, nonpharmaceutical interventions continue to be the best preventive tools. Transparent, contextualized messaging and embracing uncertainty are essential while science moves forward. Currently, there are too many research gaps to conclude that masks offer benefits beyond reducing transmission risk. We should not advocate for these benefits without fully comprehending the risks.

 This back and forth lacks fundamental reliable data. The latter states that masks may work preventing an infected person infecting others. Whereas the former seems to rely upon masks no matter what. Despite the Politicians relying on Science, science by its very nature is Hegelian, thesis, antithesis, synthesis. And then we start all over again. The paradigm of mask wearing has clearly become a political statement. It is the Tricolore of the Jacobins, wear it or get beheaded. 

It would be worthwhile to have some reasonable studies. Not academic one offs, such as photographing a sneeze. Aerosols are real, but they are also quite complex. Newtons laws fundamentally apply, assuming we can account for all the forces, downward and upward. Thus if an aerosol contains warm air from the lungs of an infected person, in the winter the warm air is much less dense than the cold and thus this particle "floats" on the denser cold air. Archimedes knew this in his bathtub on Sicily millennia ago. Our "scientists" seem clueless regarding this, at least for publishing results.

Thus should we wear a mask? Like Descartes and others, it is akin to believing in God, what do you have to lose.

Stark Contrast

 In 1968 I was at MIT. The election was highly contentious with Nixon vs Humphrey. The summer of 1968 was bedlam with the Chicago Police smashing protesters in Chicago and after the assassinations of MLK and RFK.

Jerry Wiesner was the President of MIT and the draft was a very real option. Jerry kept the MIT ship afloat and stable, managed to avoid the Harvard problems, and despite the SDS and other terrorist groups who bombed Universities, we were relatively stable. Jerry treated us as adults and expected us to act accordingly.

Now some fifty plus years latter the President of MIT writes:

In the coming weeks, I hope we will remember this feeling of pulling together – because, for all that we have in common, we do not agree on everything. As the election nears, it is important to acknowledge that the great global family of MIT includes people with a wide variety of political views. By definition then, however the coming election turns out, some members of our community will be disappointed, heartbroken, angry. If the issues at stake feel fairly distant to you, please know that there are also members of our community who fear direct, disturbing personal consequences in their daily lives.

Yes, he assumes the students, faculty and staff are a bunch on over-privileged children who will whine and cry at the least instigation. Is there as basis for this? I believe so. The change in universities have made them less institutions of leading research and more locations for self indulgent children. 

I suspect our putative adversaries are more comfortable each time people like this push the boundaries ever so more in the direction of wanton childhood.

Well We Thought So

 New Jersey demands all vote with mail in ballots even if you go to a poll, if you can find one. Now MIT has noted:

In elections, every vote counts. Or should count. But a new study by an MIT professor indicates that in the 2016 U.S. general election, 4 percent of all mail-in ballots were not counted — about 1.4 million votes, or 1 percent of all votes cast, signaling a significant problem that could grow in 2020. The study quantifies the range of reasons for this, including late-arriving ballots, problems with ballot signatures and envelopes, and improperly marked ballots, among other things. “Mail ballots tend to have more mistakes on them,” says Charles Stewart, a professor in MIT’s Department of Political Science and author of a paper detailing the study, which looks at data from all 50 U.S. states.

 Thus 4% is what we would expect in NJ or even more. 4% itself is a massive swing in votes and makes any election quite suspect. In addition in NJ one has no idea if one's vote is rejected. Moreover massive mail in voting especially in Democrat states may or may not make a difference in Presidential but will do so in Congressional.

Immunization Strategies

 When asked recently the Governor of New Jersey fumbled his articulation of the State plan, if there is one, for distribution of immunizations. The CDC put out a plan but the plan has many gaps needing completion. For example:

1. Phasing: There is essentially three phases. Phase 1 is critical workers such as physicians, nurses, Fire and Police, LTC staff and residents. Phase 2 is possible at risk such as those over 65 but relatively healthy, teachers, and those required for general economic welfare. Phase 3 is everyone else.

2. Distribution: How does the vaccine get from the manufacturer to a point of delivery?

3. Points of Delivery: Where and how do we deliver the vaccine to people. If we had a good Public Health system we could have used that for all Phase 1. Phase 2 and 3 could access it as we do now with flu shots; local drug stores.

4. Scheduling: How do we schedule the people? Phase 1 seems simple if and only if we had Public Health folks. Phases 2 and 3 can be done by Internet scheduling as is done with flu shots. However one must beware of baseless assumptions like everyone having and understanding Internet access.

5. Tracking: Since the corona virus has limited immunity we must be certain we drive infections to zero meaning annual immunizations. It also means testing. Thus, despite the concerns, we should photo each patient and give them an identity card showing what and when they were vaccinated. I had mine from 1949! Still do. Then this can be used possibly for travel, domestic and international.

6. Testing: Testing must continue unabated. That means massive random tests and not the type today. Percent positives are totally meaningless unless we randomly test a very large sample.

Just some thoughts.

Herd Immunity: NOT

 The NIH has published a piece reflecting the possible leak of long term immunity to COVID-19 infections. They note:

The new findings show that people who survive a COVID-19 infection continue to produce protective antibodies against key parts of the virus for at least three to four months after developing their first symptoms. In contrast, some other antibody types decline more quickly. The findings offer hope that people infected with the virus will have some lasting antibody protection against re-infection, though for how long still remains to be determined. In one of the two studies, partly funded by NIH, researchers led by Richelle Charles, Massachusetts General Hospital, Boston, sought a more detailed understanding of antibody responses following infection with SARS-CoV-2. To get a closer look, they enrolled 343 patients, most of whom had severe COVID-19 requiring hospitalization. They examined their antibody responses for up to 122 days after symptoms developed and compared them to antibodies in more than 1,500 blood samples collected before the pandemic began. The researchers characterized the development of three types of antibodies in the blood samples. The first type was immunoglobulin G (IgG), which has the potential to confer sustained immunity. The second type was immunoglobulin A (IgA), which protects against infection on the body’s mucosal surfaces, such as those found in the respiratory and gastrointestinal tracts, and are found in high levels in tears, mucus, and other bodily secretions. The third type is immunoglobulin M (IgM), which the body produces first when fighting an infection.

 In the limited data on patients I have seen it appears that some form of immunity may exist for several months but that the Ab do drop significantly. If that means loss of any immunity then what we have is a disease that requires annual, at the very least, re-immunization.

Herd immunity does not exist in the classic sense. Simply, reinfection is possible and we have seen that already. However the reinfections are often with "mutated" virus RNA. One could assume that the elegantly engineered corona virus may have been designed that way but that would be mere speculation. 

Notwithstanding, any suggestion that we rely upon herd immunity is not only specious but harmful and wrong. It is worth reading the reference papers in the above article to see just this effect.

NJ 2020 10 18

 Well those little Middle and High School Petri dishes are really starting a new pandemic.Look at Morris County, 90 new ones just yesterday. No deaths but mass school gatherings, apparently initiated by the schools, basketball etc, and what does one expect. We are going backward since these Petri dishes will be sending the virus home and then everywhere! This is why real time testing and data are demanded. Each child should be tested at least weekly! I said this months ago. Testing facilities should be everywhere but instead they are closing. None of these kids wear masks, distance themselves, but just the opposite. I predict in a month at this rate we will be back in April rates. What are the "knuckleheads" in Trenton doing? Counting votes...

This is the State data, there is clearly a breakout from Lakewood and spreading. We noted this in March. Drove home last night saw East Hanover HS Football field lit up with game and large crowds. Madison Middle School has hundreds lined up unmasked doing basketball PE one would assume. In my opinion this is clearly reckless. Businesses would be closed but the Education establishment seems to believe they are exempt from the laws of Nature.

You Can't Steer a Ship Without a Navigator

There is an old joke about a German sub during WW II which lost its ability to navigate, no data. It went; the Captain sent a message to the crew that they were to surface. However, they all knew they had lost their navigator and were sailing in the dark, say to tell. The Captain said: "I have good news and bad news. The good news is we may be surfacing in Buenos Aires harbor. The bad news is it may be New York City."

 The joke is a truism, namely you don't know where you are going without data. COVID has been driven to Scylla and Charybdis due to the lack of reliable and timely data. Science writes a piece laying the blame on Dr. Birx[1]. In my opinion, she tried to fix what may be an unfixable problem often caused by the very Government itself. This Science piece is just another hit piece by the left-wing media, yes indeed. One must remember that Science was headed for a long while by a former New Jersey Congressperson. Not an arm's length relationship.

 The Science article states:

 …a top aide to White House Coronavirus Task Force Coordinator Deborah Birx, chaired the meeting. Zaidi lifted her mask slightly to be heard and delivered a fait accompli: Birx, who was not present, had pulled the plug on the Centers for Disease Control and Prevention’s (CDC’s) system for collecting hospital data and turned much of the responsibility over to a private contractor, Pittsburgh-based TeleTracking Technologies Inc., a hospital data management company. The reason: CDC had not met Birx’s demand that hospitals report 100% of their COVID-19 data every day…

 Now what is the real problem? In my opinion, it is simple, if one is trying to control a pandemic one needs timely and accurate data. Who is infected, where, when, and the like. The data must be timely, namely what one gets today is what was actually recorded yesterday. It must reflect demographic data adequate for tracking, if such be the case. Now based upon my seven months of daily tracking in New Jersey the data is notoriously corrupted. LTC never reports on weekends thus seeing spikes in the data. Infections are reported which are highly suspicious. Deaths are recorded with patients having multiple underlying problems who most likely would have dies otherwise. Bottom line, the State data is often useless. It may have gotten a bit better but State Public Health is after all just another group of State employees.

 So where does or did the CDC fit in? Frankly from the beginning, nowhere. Their data was in my opinion and in my experience inaccessible and useless!

 Now Science continues the attack on Birx. The reality was that Birx clearly knew the criticality of data and that the CDC had been grossly incompetent in gathering and disseminating the data. The hit piece then states:

 CDC employees with whom Science spoke—who requested anonymity because they fear retaliation—along with other public health leaders, say Birx’s actions, abetted by a chaotic White House command structure and weak leadership from CDC Director Robert Redfield, have contributed to what amounts to an existential crisis for the agency. And her disrespect for CDC has sent morale plummeting, senior officials say. During a May task force meeting, The Washington Post reported, Birx said: “There is nothing from the CDC that I can trust.”…

 The statement has a great deal of merit. The clear evidence was the CDCs lack of an operational plan, the incompetent execution of testing, and the gross failure to address the pandemic when it was well known even in mid-January! The article continues:

 Agency insiders concede that CDC’s National Healthcare Safety Network (NHSN)—the system used for 15 years to gather crucial data from hospitals—was far from perfect. The network, which collects data from about 37,000 hospitals and other health care facilities, has been underfunded for years. All the same, five times weekly, NHSN reliably produced actionable COVID-19 data such as available hospital beds, intensive care occupancy, and ventilators used, according to CDC sources and internal reports obtained by Science. CDC staffers used long-tested statistical algorithms to impute missing data….

 This is in my opinion another understatement. I tried on multiple occasions to access the data to no avail. The New jersey data was accessibly every day, no five day routine like the lazy CDC. A pandemic is an all hands on deck action, forget Saturday and Sunday folks. The Science piece continues:

 Birx’s imperative of 100% of hospital data every day has proved elusive. The Department of Health and Human Services (HHS) data hub for hospital capacity, including inpatient beds occupied overall and by COVID-19 patients, now draws on data collected by TeleTracking, a for-profit company with nearly 400 employees, and on data submitted by state health departments and hospital associations. As with NHSN, nearly all data are collected manually rather than automatically from electronic patient records. Some hospital associations and health departments combine data from hospitals into spreadsheets and send them by fax or email to HHS. TeleTracking also offers a web interface for hospitals or their contractors to enter data.

 Yes indeed the data is corrupted by inconsistent and highly error prone methods. As anyone knows who has dealt with hospitals, even the best of University related hospitals the MIS and data folks and decades behind and getting data is akin to the proverbial extraction of hen's teeth. It is not only hospitals but the needs to test and report. CDC was initially relied upon for testing and in my opinion they grossly failed. That was problem number one. Then everything else was catch up. We are still playing catch up.

 Just look at the disease cycle. Someone gets infected. It takes a week before symptoms, three days before testing, three days to get the result and thus an infected person is spreading the virus for almost two weeks! Then the data gets reported and finally sent to a master database. The result is a delay which will make any control system grossly unstable. One can just look at the Lakewood NJ mini pandemic. We knew it would happen and it took more than a week to sound the alarm. A proper data collection system is critical but after decades CDC has done nothing to implement it. Birx tried to repair the wings of a stricken aircraft while flying at 40,000 feet! The hit piece continues:

 The underlying data tables are updated daily but run 3 to 4 days behind—less efficient than NHSN before it ceased operating. CDC officials and public health experts blame several factors for those problems: Hospitals aren’t used to TeleTracking’s system and the additional data points (such as age) added work. Also, TeleTracking has long-standing relationships with fewer hospitals than NHSN; such relationships can speed troubleshooting.

 Reporting to CDC works with reportable STC, rabies, Ebola and more classic results. A three day delay in a rabies report is not a serious problem since the patient is being treated. Three to four days with STC is not that bad nor is HIV in today's world.

 It is regrettable that this hit piece is an ad hominem attack and fails to address the true scientific issue. What should be measured, how, when, by whom, etc. This is as simple problem but one of scale. Moreover, the data MUST be transparent and publicly available. Unlike prior times we now have many competent individuals and groups whose analysis of the data can be complementary. The CDC had a long history of deliberately making their data inaccessible and grossly lacking in transparency.

 Regrettably this article seems politically motivated and missed the opportunity to define the problem, suggest solutions and help remediate what in my opinion is a broken organization.

---

[1] https://www.sciencemag.org/news/2020/10/inside-story-how-trumps-covid-19-coordinator-undermined-cdc

NJ 2020 10 16

 Let us take a look at the hot spots. There is an increase but it is highly focused. First the county and town numbers. We see a one day blip but there is a rather constant daily incidence of some 40 cases per day for the county.

Below is the daily increase and we see again the noisy nature of the data. Thus any single day is meaningless.

The town prevalence is below. As I have repeatedly noted the schools not only allow but seem to mandate teen age clusters which are petri dishes. Yet the teenagers have mild is not obvious disease presentations but are voracious spreaders.

The county stats remain with three major clusters. Nothing much has changed.

Now Ocean county is grossly different. Here in Lakewood we have 10X Morris county's worst! Moreover the surrounding towns have massive spread.

This chart below is mortality rates. The highest in Manchester is over 16%! The same for all surrounding towns. Thus not only do we have high incidence but massive mortality rates!

You can see the location in the map below, it is a cluster around Lakewood.

The state cases are on the rise but for the most part driven by this cluster.

You can see Morris county remains flat.

Overall deaths are low, but dominated by this cluster.

The closer look below shows the more than doubling of daily incidence since mid June. It was relatively flat until the Lakewood cluster exploded.

Deaths continue in LTC facilities and again that is grossly unreasonable.

NJ 2020 10 15

Current NJ by county as of today. My guess is that we have a massive explosion due to teenage kids. They are all out on school grounds playing sports. Colder weather will force them indoors and make it worse. The good news is deaths are minuscule. It is becoming a flu like disease.

Science, Scientists, and Politics

Both Nature[1] and Science[2] have come out to support the Democrat and to be repulsed by the Republican. Not having a horse in this race, I felt it was worth commenting upon the now grossly political nature of these long-time bastions of scientific facts. I have noticed since the Vietnam days that these organs have slowly morphed into political and policy documents which from time to time present compelling scientific insights. Let me address just a few issues;

 1. COVID-19: Science states:

 At home, Biden says he’ll work with governors and local officials to encourage greater use of physical distancing and masks—possibly even mandating their use at federal facilities and on federal lands. And he’s vowed to reverse the erosion of public trust in two key health agencies, the Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA), by appointing new leadership and improving the transparency of decision-making.

 Let us examine the facts. The CDC lost public trust because of its own gross incompetence. As we have noted before on multiple occasions, we publicly knew the pandemic was upon us on January 29^th with the publication in NEJM of the articles detailing the Wuhan epidemic. That was the clanging bell. Ironically from January 16 through February 6 the White House was engaged in the House initiated impeachment trial. Needless to say, a distraction but it should not have distracted the CDC. One must remember that most of the "leadership" of the CDC was a remnant of the previous administration. As to the FDA, is has a long reputation of being glacial in its movements, and often for good reason.

 2. Iran: Now strangely this is an area that one surmises that Science has little to no expertise but regardless they opine:

 Biden will move aggressively on several fronts. Many want the country to re-engage with Iran to revive the nuclear deal—from which Trump withdrew in 2018—that limited its ability to produce nuclear weapons. Biden says he will “offer Tehran a credible path back to diplomacy” if Iran “returns to strict compliance with the nuclear deal.”

 My first experience with Iran was in 1979. We were working on the Comprehensive Test Ban Treaty, CTBT, and building the seismic sensing network, Units were to be installed in northern Iran and people were in place when the Shah fell. Needless  say they got out, by the hair of their teeth. Iran is a political time bomb, a clear and present danger, and putative nuclear threat. Trust goes just so far. It is clear that having isolated Iran has allowed a coalescing of the Arab states. That leads to a more stable bulwark against the Iranian nuclear threat.

 3. China: Here I have a real issue. They state:

 Another tough challenge will be establishing the rules for U.S. research collaborations with China. Under Trump, law enforcement agencies, the National Institutes of Health (NIH), and other agencies have stepped up investigations of scientists who failed to disclose funding ties to foreign institutions, leading to criminal, civil, and administrative punishments. Many of the known cases involve researchers who were born in China or had links to Chinese institutions. Critics say the effort has been racially tinged and has also hindered efforts to recruit foreign-born talent. They hope Biden will ease the scrutiny. But Biden has traditionally been a defense hawk, and China’s harsh treatment of Uighurs and other religious minorities may limit moves to ease tensions.

 China is a massive political, economic, and military threat. One need do nothing more that re-read Mahan and his works on Pacific Oceanthreats. Mahan was a household name in Germany and Japan before WW II and even today in China. China has used the US as a stepping stone to both economic and scientific advance. While back at MIT from 2005-2012 I had the opportunity to deal with many mainland Chinese students. Very bright and being funded by such agencies as DARPA. Yes, our Military was funding a possible adversary! As they say, you cannot make this up. Most if not all returned elsewhere, taking with them invaluable information, contacts, and motivations for their home country. It was in the Clinton administration that the US first opened the door to massive technology transfer, legal and otherwise. It was a direct result of this open-door technology transfer that China managed to build Huawei, while companies such as Motorola who gave them the opportunity languished.

 The greatest threat may very well be in the life sciences. China has clearly leapfrogged generations and is now on an almost equal standing with the US in terms of the biosciences. One need look no further than the literature in the field of various cancers and related therapies. This of course is a double-edged sword as we see from the current virus.

 Should the US be wary of China and its scholars? Were we equally wary of Russian (Soviet) scholars? The answer is clearly in the affirmative.

 4. Universities and Spending: The driver one suspects for this support is the promised increase in University support. Specifically, they note:

 Keeping the economy afloat through the pandemic will require massive federal spending, Biden says, and he will likely ask lawmakers to approve a host of spending initiatives early in his term. Universities and research groups want some of the money, saying federal science agencies need tens of billions of dollars to help them recover from the pandemic.

 However, one wonders what Universities have done to merit such support. In World War II, MIT and U Cal, Columbia, U Chicago and many others banded together to develop radar, weapons, and other strategic elements that allowed us to overcome the monsters who were destroying mankind. Since Vietnam, universities want money but seem to think there is no obligation to assist the nation. Where was the Rad Lab equivalent at MIT? Nowhere, in fact there was blatant opposition to anything supporting the effort to overcome the viral attack.

 In contrast, it appears that we have great strides in therapeutics and vaccines, all from private industry. In this war against COVID, industry has stepped up with massive Government funding and most likely will deliver a vaccine early next year. Consider what Government has not done, no Ebola or AIDS vaccine. After billions of Government spending, and decades of AIDS effort, NIAID has delivered nearly nothing in AIDS and limited amounts in Ebola and other pandemic viral infections.

 5. Government Workers: One must remember that there are millions of such workers. High Tech has siphoned off many highly competent people as has industry. The Government gets what is left.

 Under Trump, many researchers who work for the federal government have said they don’t feel valued or respected. Employee surveys show job satisfaction at several science agencies has taken a nosedive, and there have been many anecdotal reports of researchers leaving their jobs. Biden says he wants to reverse that trend, starting by replacing Trump appointees who have suspect scientific credentials or hold views far out of the mainstream. “The house cleaning could be remarkable; in some cases you are going to see hacks who are flat-out science deniers replaced by appointees who not only understand the science, but have done it themselves,” says one lobbyist who requested anonymity because he still interacts with the Trump administration.

 Government workers for the most part act as intermediaries. NIH does fundamental research but it also acts as an administrative organ managing external research funding. The "hacks" that the writer notes have always been with us. I have seen first hand in the Carter Administrations many such hacks. Go from one administration to another and the cast of characters may change but the characteristics do not. The "Plum Book" is an example of the list of the many favored positions given to supporters and their related friends. Our Government has always been populated at the high levels by political types.

 Overall, the reasons noted have multiple facets. There is no clear path, some good and some not so good. Yet scientists must learn that this is the essence of politics…perhaps why Washington gave them a swamp for the Capitol.

---

[1] https://www.nature.com/articles/d41586-020-02852-x

 [2] https://www.sciencemag.org/news/2020/10/biden-presidency-could-have-remarkable-impact-science-policy-also-face-hurdles

 

Some Data from NJ

 This is the current death stats from LTC and non LTC. Almost a 50:50 split. Just in case anyone wonders.

Facts and Statistics: The Book has yet to be written.

 There were two articles in JAMA allegedly estimating the excess deaths from the current virus. The first article noted:

Between March 1 and August 1, 2020, 1 336 561 deaths occurred in the US, a 20% increase over expected deaths (1 111 031 [95% CI, 1 110 364 to 1 111 697]). The 10 states with the highest per capita rate of excess deaths were New York, New Jersey, Massachusetts, Louisiana, Arizona, Mississippi, Maryland, Delaware, Rhode Island, and Michigan. The states with the highest per capita rate of excess deaths changed from week to week. The increase in absolute deaths in these states relative to expected values ranged from 22% in Rhode Island and Michigan to 65% in New York. Three states with the highest death rates (New Jersey, New York, and Massachusetts) accounted for 30% of US excess deaths but had the shortest epidemics (ED⁹⁰ < 10 weeks). States that experienced acute surges in April (and reopened later) had shorter epidemics that returned to baseline in May, whereas states that reopened earlier experienced more protracted increases in excess deaths that extended into the summer.

The second article alleges:

 Compared with other countries, the US experienced high COVID-19–associated mortality and excess all-cause mortality into September 2020. After the first peak in early spring, US death rates from COVID-19 and from all causes remained higher than even countries with high COVID-19 mortality. This may have been a result of several factors, including weak public health infrastructure and a decentralized, inconsistent US response to the pandemic.

Now here are four major concerns:

1. In New Jersey, and one suspects in New York,  as we have reported here almost daily, half or more than half of the deaths were in long term care facilities. These were the direct result of sending a few infected patients there as well as not testing care takers. Thus this number of deaths is less a result of the disease than of the lack of moral attention given these facilities by the State.

2. From about March 15 through June 15th in New York City, the Emergency Departments were empty of normal patients with heart attacks, strokes, and other common causes of death. So where did they go? Did more die of these causes for lack of treatment. Who signed the death certificate and what was the cause the virus?

3. Co-morbidities added to the mortality. It was not just age but such things as obesity, Type 2 diabetes, congestive heart failure, and other sever co-morbities may be exacerbated by the virus and treatment for the co-morbidities delayed.

4. Patients with cancers, for example failed to get care during the four month window. Now  early prostate cancer is not a problem but melanoma and hematological cancers can spread rapidly and become terminal.

 Thus one must adjust the numbers to reflect at least these significant factors. There does not appear to be any attempt no less even recognition of these factors.

We suspect that it is thus too early to make statements of the type in these two articles. post hoc analyses will take a few years after proper data collection and analyses. It is regrettable that we will undoubtedly see these numbers floated in some political campaign most likely. Epidemiological analysis requires detailed study of all the facts. Unfortunately we are not even close to having them.

And unsurprisingly the Press seems to take the results presented at face value without any consideration of the failure to address the few issue above. The real question is: how many deaths from unpreventable COVID-19 alone occurred. Then one must ask; how many deaths resulted from failures in treatment, and then one may have a glimpse at the true facts.

And You Think We Are Confused Now?

 The NY Times has a piece on the complexity of distributing the collection of vaccines for the current virus. They note:

In a phone call with reporters on Friday, Paul Mango, an official at the Department of Health and Human Services, said that Operation Warp Speed was on track to have up to 700 million doses of various vaccines by March or April — enough, he said, for “all Americans who wish to get it.” As for who would get which vaccine, he said that would be left up to the Centers for Disease Control and Prevention’s vaccine advisory committee. “They will guide us as to which vaccine is most appropriate for which class of Americans,” he said. But the advisory committee doesn’t have a plan for that yet, and Dr. Grace Lee, a professor of pediatrics at Stanford University School of Medicine and a member of that committee, warned it would have a hard time coming up with one. “It’s tough to do, given all the uncertainty with Covid vaccines,” she said.

Now this is truly terrifying. If we have a change in Administration then it will delay everything six to twelve months. If we do not, then we have to deal with the present confusion.

Yet the worst part is that the CDC is still "in charge".  Their gross incompetence in my opinion means that one should not expect anything. We really should have a more competent and transparent entity. If we rely upon state Governors to do anything it will again turn into a political quagmire of bumbling politicos. 

Here is a chance for a great hand-off from the developers to the Public Health folks. My suggestion, let CVS etc handle this, keep it out of the CDC, they could not plan a birthday party. Unfortunately this will not happen and we will be back here six months from now bemoaning the problem.

If You Really do NOT Want my Vote: Call Me!

 This is the season of annoying nonsensical robocalls from politicians. I really do not know who told them if they robo call at dinner time that they will get a vote. NOT!

The same goes for sampling potential voters. Who in their right mind would tell some caller what you intend to do? It could be some Russian operative, or worse, a Chinese Restaurant checking on your order!

Thus Polls have become of zero value. We saw that in 2016, it will be interesting what happens this time. Please stop with the calls.

NJ 2020 10 10

 Things are not going well. Saw over a hundred middle school kids at local basketball court all lined up and mask-less. They were there for hours for what I gather was some PE event. Do our educators have a clue?

First the Ocean County explosion. Wonder what County Health Offices are really doing.

The chart below is the Morris County and Florham Park numbers.

The graph below is Florham Park, still low simmering most likely the schools.

The chart below is Morris County Town stats. Still same hot spots.

The State is below. Dominated by Ocean County.

Morris County with a blip but steady low infection rate.

The infections per PoP per County. Ocean is a real mess, Lakewood seems the focus.

Here is Ocean by day. It may be slowing.

Mortality is low. It seems to almost disappeared as compared to earlier.

The is new infected per day. This is the most worrisome chart. Look at Ocean as the driver.

This is the death chart by LTC and non LTC. Why we still see LTC deaths is beyond reason.

I am an Ockhamist

William of Ockham stood at the middle of the 14th century, addressing first the re-assessment of Aristotelian and Platonic epistemology and linguistics, examining the theological standing of the Avignon Papacy and ultimately dealing with the rights and duties of individuals. Ockham was influenced by Roger Bacon, whose focus on facts and not just logic, were the foundation of the beginning of modern thought.

An erstwhile Kantian philosopher has espoused in the NY Times the following[1]:

Because Mr. Trump contributed to the illness and death of so many Americans, it is understandable that many feel satisfied in seeing him forced to contend with a harm to which he has exposed so many others. The moral complexity becomes greater still when we consider that from a purely consequentialist point of view, there are reasons to view Mr. Trump’s potential incapacity as the best moral outcome. Most famously associated with the utilitarianism of Jeremy Bentham and John Stuart Mill, consequentialism is the philosophical position that affirms that what is morally right is whatever makes the world best in the future. If one believes that Mr. Trump has unleashed a tremendous amount of suffering and death through his mismanagement of the coronavirus pandemic and that he is likely to continue causing harm on this scale, a consequentialist argument can be made that his speedy recovery from Covid-19 would not be the best moral outcome.

Now, one must deal with the facts not just with the abject hatred that so many harbor. Let me begin with the author's first and last sentence.

1. The source of the virus as admitted by the Chinese was Wuhan in China and their admission was made on 29 January 2020.

2. The virulence of the virus and its transmission was likewise admitted by the Chines on 29 January, 2020.

3. On February 4, 2020 this was seen as a pandemic as I had noted herein.

4. The CDC, a multibillion-dollar agency of the Federal Government, has both the duty and responsibility to deal with such pandemics.

5. The CDC was grossly unprepared and apparently total unable to deal with the pandemic. The classic example was the deficit of PPE and more the case of materials to validate infections.

6. The President is neither an expert in pandemics nor in public health.

7. The US is a Republic meaning that Governors typically have major public health responsibilities, hopefully with guidance and support from the CDC. Neither seemed to work.

8. In New York and New Jersey, the majority of deaths were in my opinion based upon the available evidence a direct result of Governor's decisions to move infected patients into nursing homes. It was akin, in my opinion, to the US Army sending smallpox infested blankets to Indian tribes in the 19th century. The sad fact is that in New Jersey this seems to be a continuing source of mortality. One must remember that the US is not like France, England or China. The Republic nature delegates significant responsibility and thus blame to the States.

9. Thus, the source of the death and suffering must be shared across a wide group of fumbling and politically focused individuals and organizations.

10. The source of the problem is not singular, but a complex set of human factors, local, State, Federal, and international. Clearly if the CDC and the Federal Government had a plan, we never saw it. Perhaps the States did but it is not clear how they handled the issue, other than counting deaths in long term care facilities.

Kantian's fundamentally ignore the biological factors that make humans act. Admittedly Kant was unaware of them more than two centuries ago but perhaps we have learned. Regrettably we will not learn anything from this pandemic perhaps for a century or more if we wallow in the quagmire of political unrest. In my opinion this rather sophomoric morality tale is without merit. We truly need rational minds based on an ever-changing set of "facts" to make beneficial societal decisions. Regrettably we seem stuck in a Roman Circus, with battling gladiators and cheering crowds whenever more blood is shed. 

[1] https://www.nytimes.com/2020/10/09/opinion/trump-covid-shadenfreude-ethics.html?action=click&module=Opinion&pgtype=Homepage

Galen and Hard Facts

 COVID-19 is an elegantly engineered virus, by nature or by man. It not only attacks the pulmonary system but is systemic, most likely via an explosion of the immune system, innate and adaptive. My guess, TLR-7 and IL-6, but time will tell, Along comes a writer in Science Translational Medicine who notes:

The New England Journal of Medicine today has the final report from the team studying remdesivir in a >1000 patient randomized controlled trial. This group was randomized and divided roughly half-and-half to standard of care plus remdesivir versus standard of care plus placebo, blinded. So this is the most solid look we have at the drug’s efficacy in coronavirus patients. The good news is that the patients receiving the drug had a shorter time to recovery (9 to 11 days, in the 95% confidence interval, versus 13 to 18 days with non-remdesivir standard of care. That’s real, but it’s not real dramatic, either, which is what you would realistically expect from a single broad-spectrum antiviral drug. This ain’t sofosbuvir clearing out hepatitis C, and even that one doesn’t do the job by itself. As for the hardest endpoint of all, mortality by Day 29 for these patients was 11.4% with remdesivir therapy as compared to 15.2% with the controls. So again, that’s a real improvement and very much worth having, but it’s not a Miracle Drug, either.

Frankly no surprise. This elegant virus demands a Cocktail approach. We said that in early April. Thus any criticism of this therapeutic agent alone is baseless in my opinion. Oncologists have known now for half a century that one must treat the full chain of events, assuming one knows them.

Thus, in my opinion, I would strongly suggest a criticism of one therapeutic is meritless. But I guess someone must fill the web site with something.

Where is Ockham When we Really Need Him?

 In the China Digital Times they note:

The Vatican has decided to extend a secret 2018 agreement with Beijing that governs the appointment of bishops in China. The 2018 Sino-Vatican deal, signed in the midst of crackdowns on religious expression, is believed to give Beijing the power to appoint Catholic bishops, pending the Pope’s final approval. This follows news that Chinese hackers gained access to Vatican networks before the start of negotiations on the deal’s extension. For the AP, Nicole Winfield reported on the consensus reached by the Pope and the Pope Emeritus on the perceived necessity of a deal with China...The P.R.C. is seemingly content with the deal. Ministry of Foreign Affairs Spokesperson Zhao Lijian said, “the interim agreement on the appointment of bishops between China and the Vatican has been implemented successfully.” In a speech delivered on the 150th anniversary of Italian Catholic missionaries’ arrival in China, Cardinal Pietro Parolin, the Vatican Secretary of State, argued that the deal was purely pastoral, not political, and that it would prevent the illegal ordination of bishops by Chinese authorities.

Avignon, when the Church had three or more simultaneous "Popes" was the last time we saw countries control the Church. It was Ockham who saw this as a sign of heresy and frankly he had a point. The Bishop of Rome and the PRC seem to walk arm in arm as contrast to John Paul II.

COVID-19: Facts and Dates

 Just to make certain everyone knows, on 29 January of this year in The New England Journal, two articles were published:

A Novel Coronavirus from Patients, with Pneumonia in China, 2019

In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing.

and

 Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

 On the basis of this information, there is evidence that human-to-human transmission has occurred among close contacts since the middle of December 2019. Considerable efforts to reduce transmission will be required to control outbreaks if similar dynamics apply elsewhere. Measures to prevent or reduce ransmission should be implemented in populations at risk. 

Now one must wonder who dropped the ball here. Timelines often tell the entire story. Most people think we did not know until two months latter. Read the last sentence above, I had.

Cogratulations for CRISPR

 The two scientists who discovered the CRISPR functions were awarded the Nobel Prize in Chemistry. Congratulations!

Back in 2014 I wrote a piece on CRISPRS and Cancer but before that I had a chance to lecture on botany to my grandchildren's class, I believe it was third grade. I spoke of plants, gave  them seed and at the end I told them about CRISPRS. Paralleling the Graduate and Plastics, I told these wide eyed Third Graders that their world would be with CRISPERS, forget plastic.

I often wonder if any took the bait. Perhaps today may awaken a few. So congrats to Emmanuelle Charpentier and Jennifer A. Doudna.

Well Here Goes

 

Off it went to the official Ballot Box. Now what chance do I have to have my vote counted. Think of what can go wrong. First it may never get collected. Then it may be damaged. Then they may reject my signature, which is a good chance. Then it may get mislaid somewhere. The list goes on. But it is New Jersey so who cares. Just raise the taxes, close us all down, except for certain Country Clubs.

NJ 2020 10 03

 Looks like it is starting all over again. Here is Ocean County and Lakewood continues to explode. Perhaps a total quarantine is needed. Below is the per PoP for Ocean.

This drives the entire State as we see the rise in the tail.

The good news is the very low mortality.

Our County still has a tail but no where near Ocean

But the State is really going up again!This does not bode well.

Again Lakewood but the total increase.

Compare to Morris with the three smaller and persistent hot spots

County and town comparisons. Town has been flat for two weeks as shown below in prevalence

County shows a flat daily driven by 3 towns.