Pandemicland

We are well over the one-year mark on the global COVID-19 pandemic. Progress is uneven. The U.S., for example, spent much of the last year at war with itself over basic scientific common sense. Instead of embracing cost-effective protocols like masking and social distancing, right-wing elements of the U.S. chose instead to paint measures as violations of constitutional freedoms (they are not) and invented an unnecessary culture war. While private companies, in some cases in partnership with public or academic institutions, raced to develop vaccines, societies fractured and only managed to provide aid and comfort to a deadly virus.

The U.S. is in a strange equilibrium. You can see it in the data. Mutant variants of the SARS-CoV-2 virus … some more deadly and far more transmissible than the original strains … are widely becoming the dominant infectious versions. Meanwhile, vaccines are beginning to prevent serious disease and death in the most vulnerable populations (the elderly, for example). Working against the vaccines, people are going around unmasked in closed spaces and with reduced social distancing while also expressing resistance to vaccination or vague “hesitancy.” These conflicting forces appear to result in a tension between the virus (its relentless drive to infect and replicate), driving up cases, and medicine, driving them down. We are in a weird stalemate.

CDC data on new cases (blue and red lines) and deaths per 100,000 people (yellow line). Death and new case rates are nearly comparable to the peak of the second wave in the United States about 1 year ago, despite massive advances in vaccines.

Compared to a year ago, we really know how to fight this virus. There are at least 4 well-established vaccines against SARS-CoV-2, including more recent mutant strains. There are even more vaccines than just those 4 in wide circulation, but their efficiency is not as well-established. Nonetheless, a year ago there was not a single vaccine. We still lack medical treatments that definitely prevent death or reduce infections, apart from vaccines. A lot of therapies, like monoclonal antibodies or antiviral agents, have never been convincingly beneficial. Hospitals have a battery of interventions to help patients survive, including oxygen and the prone position during the worst stages of the disease. Social distancing and masking have proven to be the most effective strategies in the absence of a vaccine, but right-wing organizations created fake controversy about those approaches and led about a third of the population to rebel pointlessly against their use.

As India plunges deep into its worst medical crisis, no doubt now (like Brazil before it) a hot bed for viral mutation as SARS-CoV-2 spreads almost unchecked through society, we enter a terrifying new global phase of the pandemic. India, once poised to be a major producer of vaccines, now desperately needs to import therapies as it drowns under an unchecked case load. Meanwhile, in the U.S., the rate of new cases per day and even deaths rival the “second wave” that happened last summer. We’re nowhere near the peak in the bleak winter months, but we are still Pandemicland.

I myself was fortunate enough to receive a Pfizer vaccination through SMU. I was first able to sign up when vaccination was opened up to all adults. My first shot was about four weeks ago and my second about one week ago.

I was so happy to have a reaction to the second shot. About 14 hours after receiving it, I developed flu-like body aches. That was it. I took some acetaminophen every 8 hours, rested after my work day ended, and woke up the next morning feeling normal. My body had produced coronavirus spike protein and my immune system attacked. It was glorious. I am now part of a system of vaccinated people who help to block the spread of this deadly virus. Together, we protect each other and especially those who cannot get the vaccine or who, even when vaccinated, are still at high-risk.

Top: new cases per day in Collin County (purple and pink) and number of tests per day (blue). Bottom: significant events in Collin County that might affect the spread of the virus. The lines indicate the day of the event and the colored band about 2 weeks later indicates when we expect effects to appear in case data.

I am just one of about 40% of people in my county (Collin County, TX) who have been fully vaccinated. I’ll reach full efficacy in about 1 more week. “Herd immunity,” when enough people are resistant to the virus sufficient to break the chain of transmission, is still very far away. We have no prior experience with this particular virus, but estimates would suggest herd immunity in a local population will be achieved when 80% of that population is vaccinated. Collin County is only half-way to that point, almost 5 months after vaccination began in earnest in the U.S. Other parts of the U.S. are further ahead, some further behind (the South in general lags the pack). However, we cannot expect vaccination to accelerate. In fact, the evidence suggests that the U.S. now has more supply than demand as we hit the core of people who reject or hesitate to get the vaccine. This alone may keep us a Pandemicland for a very long time.

The vaccine is easy. You get it, you have about 1 day of flu-like symptoms if you have a robust response to the process, and then it’s done. You can now fight SARS-CoV-2. It’s just about the simplest thing you can do besides masking and social distancing. And if you want the country to stop being Pandemicland, you need to get the jab now. If you’re not vaccinated, then you’re just one more opportunity for the virus to infect, mutate, and spread. Don’t let yourself be used by the virus.

1/6

Since Wednesday, I, like most Americans, have been trying to make sense of the events of that day. I find it’s usually best to begin with the facts, so that’s where I will start this reflection.

Wednesday was to be devoted to proposal writing. After reading the newspaper, then eating breakfast, and a morning walk with Jodi, I settled into writing. I spent the next several hours in an effort that resulted in 10 pages, when only 3 were necessary. This is how I work: get it all down on paper and worry about condensing, compressing, and editing it later.

I got so deep into this work that I tuned out the world. Mostly, that was intentional; my phone was muted, social media was safely tucked out-of-sight, and all that I had to keep my attention was Overleaf and a stack of references and ideas. What do I mean by “mostly intentional”? Well, I was scheduled to meet with a Dean at 2pm and completely lost track of time. When I came up for air (and email) at 2:40pm, I realized my mistake and panicked. While I raced to email the Dean and try to connect with them, I noticed the news notifications on my phone.

There were many … more than usual. I am used to a few breaking headlines every day from the Washington Post app, but this was way above and beyond a typical day. Of course, we know why … it was not a typical day.

Thousands of enraged devotees and disciples of President Trump, their anger stoked by the President’s rally in front of the White House, marched on the U.S. Capitol Building. Hundreds, if not more, pushed through police who seemed to do the minimum required to keep them back and smashed their way into the complex. Senators and Representatives were whisked to safety or sheltered in place. There was gunfire. Chemical agents were deployed by police and by the fascist crowd storming the legislative branch, looking to overthrow the results of a free and fair and verified election. Waving a myriad of flags, some of which actively advocate against our union of states, this traitorous mob was looking to setup a dictator in place of a representative democracy. They would have their Mad King George seated on a throne of lies, no matter what damage had to be done, or who had to die.

While these were Americans, and while they no doubt represent the worst impulses of our nation that have been with us since its founding 244 years ago, they created a moment that represented one of the clearly darkest in our history. We watched Americans assault the very foundations of the democracy that made their liberties possible in the first place.

None of this was a surprise. As many commentators have noted, it was nonetheless horrifying.

As a scientist, I have watched the slide of Americans into the darkness, fueled by credulous thinking and misinformation, for a long time now. Long before I became aware of the undoing of American reason, it had already begun. You might go back to slavery itself and note what wrong thinking led to that awful institution, whose legacy is still with us. You could point to the snake-oil salesmen and hucksters of the old west, duping the un- and under-educated public. You could point to the Scopes “Monkey Trial,” which marked the rejection of the scientific explanation of biological diversity in favor of a specific Christian theological explanation in public schools. You can point to the anti-science campaigns of tobacco companies designed to hide the health crimes of their product. You could point to the rise of fundamentalist Christians as a political movement in the late 1970s and early 1980s, aided by the Reagan presidency, and the birth of the “scientific creationism” movement – a rebranding of the movement to literally interpret the Bible and accept it as scientific fact. You can point to climate change denialism, and human-induced climate change denialism. You could point at vaccine denialism, flouride denialism, chiropractic, and alternative medicine. You can point to “intelligent design,” the “wedge strategy” of a wing of the fundamentalist Christian right, the misunderstanding of economics, or the demonization (against all evidence) of migrants or non-Christian religions.

In truth, all of those were pieces in a long-building puzzle that culminated on January 6, 2021. Each of those episodes was a test of critical thinking, one which people inevitably failed. Maybe it was few people. Maybe it was many. But each chapter was a step on the road to the credulity that fueled the rage we say on 1/6. The work of tobacco companies, for instance, over many decades to perfect the trapping of science while undermining public trust by avoiding the foundations of science, gave the public permission to think that all conclusions are equally valid. For every one scientist who finds evidence on one side, it seemed, there will be another who finds evidence on the other. This play-acting at science was designed to avoid the questions of “what kind of evidence?” and “what quality of evidence?”

If you cannot discern reliable evidence from poor evidence, then of course you will fall prey to people who make claims about quantity without reference to quality. For example, if you think testimonials are as equally valid as information gathered from records or experiments, then of course you will believe when someone says there are lots of signed testimonials attesting to, say, voter fraud or election fraud. The same movements that undermined American’s ability to discern the quality of evidence in public discourse – the creationist movement, the anti-climate science movement, etc. – allowed for the rise of a demagogue who acts only in service to himself while duping others into siding with his cause.

American democracy can resist this, of course, but only if people uphold the foundations on which it is built. As members of the legislative or executive branch act to undermine constitutional democracy by claiming fire where there is only a smoke stoked by lies, the foundation weakens. I believe that each of us is the bulwark against the fall of our democracy, each of us a candle in the night and a light against the dark. Our light is snuffed out when we fall prey to magical thinking, wishful thinking, and credulity. Our light is brightened when we accept hard truths, backed by the best quality of evidence, even when those truths run counter to our desires.

Our founding fathers were flawed, complex human beings. Among their better qualities, however, many of them understood the value of scientific thinking … even practiced it. (albeit not in all things, such as in relation to skin color and inherent value) They even enshrined the importance of arts and sciences in the main body of the Constitution, writing,

The Congress shall have Power … To promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries;

The U.S. Constitution, Article I, Section 8

They would not even enshrine some of the things we take for granted these days – freedom of speech, of religion, of the right to bear arms – until the amendments to the Constitution were passed (the “Bill of Rights”). However, promoting the progress of science and the “useful arts” was right up front in the powers of the legislative branch.

We must recognize that rekindling the light of liberty and restarting the heart of our republic will begin with a turn to science and arts, which themselves are a reflection of human reason, creativity, and expression. You don’t have to be a scientist, or even have a college degree, to practice basic critical thinking – the kind that can cast the light that will be needed to drive out the shadows that waged war on constitutional democracy on 1/6.

Photo by David Tomaseti on Unsplash

Coda

The Washington Post has compiled an excellent and terrifying video timeline [1] of the events surrounding the insurrection. It shows the rage, the violence, and the terror inflicted on the U.S. Capitol Building on January 6, 2021 … all in service of a pure lie. It also shows the heroism of security and police, even as we continue to learn more about how unprepared … and even encouraging of the insurrection … officials and parts of the police force were that day.

[1] Dalton Bennett, Emma Brown, Sarah Cahlan, Joyce Sohyun Lee, Meg Kelly, Elyse Samuels, Jon Swaine. “41 minutes of fear: A video timeline from inside the Capitol siege”. The Washington Post. January 16, 2021. https://www.washingtonpost.com/investigations/2021/01/16/video-timeline-capitol-siege/

Muon Weather and Seasons

Over the winter break, I have picked up my little muon detector data side project that started in the spring term of 2020. A few days ago, I remarked on how I wanted to take account of “weather” in the data – variations around a daily expectation given seasonal conditions – and “seasons” – long-term trends in the data.

Based on almost 290 days of data since I began this project, it was clear that the counts vary with time with short-period and long-period trends. Let us define a muon “timeblock” as a quarter-hour (15 minute) duration of data-taking. In a single timeblock, the detector typically reports the passage of about 1000 muons. What 290 days of data has taught me is what many previous experiments have also seen: there are overall fewer muons per timeblock in colder months and more in warmer months. So there is something of an annual overall trend, sinusoidal in shape, as well as shorter-term variations (hourly, daily, over multiple weeks, etc.).

Seasonal effects in muon data. The rate in a given timeblock has the average timeblock count (computer over the past 365 days) subtracted from it. “Winter-like” conditions occur when the rate is more than 1/2 standard deviation below 0. A standard deviation is determined from the the counts over the past 365 days. “Transitional” conditions (spring- or fall-like) occur within 1/2 standard deviation of the mean; “summer-like” occur more than 1/2 standard deviation above the mean.

I have now captured the seasonal effect using s sine function model. This is fitted to all previous days of data, excluding the current one, to find the best model parameters that describe the past. Today’s rate is then extrapolated from the function, including the effect of model parameter statistical uncertainty from the fitting process. This allows me to identify “weather” conditions – deviations from the daily expectations.

It is currently “winter-like” now. That means we expect, on average, the muon rate to be below the yearly average. Yesterday, we saw additionally “colder” muons weather, with quite a lull in muon counts given the expected rate in each timeblock. Today, things appear to be “heating” back to the expectation, and we will see where the day takes us.

An example of “weather” from the past 24 hours. The muon count in each timeblock has the sine function fit expectation for that day subtracted from it. We had a slightly colder snap yesterday than expected from the seasonal rate, but today it seems to have “warmed” back to normal … meaning muon counts are more consistent with the seasonal expectation today.

You can find the current muon weather at SMU on my computational lab site, SA-SO (the SMU All-Scale Observatory, my name for my virtual laboratory space at SMU): https://blog.smu.edu/saso/projects/muon-observatory/#Muon_Weather_Conditions

Muon Weather: Fun with a Muon Detector, Analysis Code, and Physics

I am spending some time playing around with the cosmic ray muon data from an instrument in the SMU Physics Department. That instrument is located in the basement hallway of Fondren Science Building. I already setup a “dashboard” of information derived from the instrument, available here: https://blog.smu.edu/saso/projects/muon-observatory/. If you want to learn more about the instrument, cosmic rays, and muons, you can check out that dashboard.

I’ve wanted to take account of the variation, over the seasons, of the muon rate through the instrument. Previous research on cosmic ray muons (there is a lot of this, since cosmic rays were discovered a century ago) suggests this variation is due to the change in temperature (and thus density) of the stratosphere over the year. More dense air = more cosmic ray interactions = fewer decays to muons.

The effect should be roughly sinusoidal, so I am trying to incorporate a sine function fit (done) into the muon rate subtraction (in progress) to better account for daily expectations. Right now, my subtraction is just of the entire running average of the count of muons, which reveals an annual variation … but fails to capture daily expectations. So, basically, I isolated muon climate (long time periods) but not muon weather (short time periods) in my current graphs … and I want to capture weather.

If you want to learn more about muons, check out my dedicated lecture on the subject from my Modern Physics course:

I’ve written extensive python and C++ code to analyze the raw data from the muon detector. That detector provides two pieces of data: the time between two pulses in the detector, and the time at which the pulses were received (e.g. wall-clock time). This is then turned into the information on the dashboard using code. This employs Panda dataframes, ZFit and ROOT to do data modeling and extrapolation/interpolation, and Matplotlib to do graphing (among other things). It’s been my fun pandemic side project since March, 2020.