THE GATHERING STORM

The sound woke me early, maybe around 5 AM, a low, prolonged rumbling. In my not-quite-awake state I thought airplane, or maybe the heavy equipment being used for the sewer project in our neighborhood. But as I gained more consciousness, I smiled...thunder, very distant thunder. 

I waited, I listened. There it was again, very low, grumbling, rolling and prolonged thunder in the distance. I finally managed to roll out of bed at about 6:00 and go to the open window. More thunder, a bit closer, and finally a few rain drops on the roof outside our window. I splashed my face with water, shrugged on a T-shirt and shorts, turned off the alarm and went out on the front porch to be in it.

Last night, late, we watched the local news to discover that our city, like many others, had demonstrators in the streets. A peaceful vigil had turned into a roving demonstration with the usual, unfortunately, vandalism of buildings - graffiti and broken windows and fires in trash cans. But this time it was different as a small group broke into the Justice Center and could be seen trashing the office cubicles. Suddenly flames appeared; they had set the building on fire. There were no police present, yet. 

The scene then devolved into what we’d been watching in other cities; roving bands of protestors, lines of armored police using tear gas and flash-bangs to push the protestors away and break them into smaller groups. People running, throwing objects, shouting, waving hand-lettered placards, shouting into the news cameras. 

Earlier in the week, a white police officer had killed a black man in Minneapolis, Minnesota. This was a public execution, one commentator called it a public lynching, as the cop leaned on the prostrate and handcuffed man’s throat with his knee for almost 9 minutes, as the victim, George Floyd, begged for help and to be able to breathe. A witnesses cell phone video has gone viral, and it is chilling. The cop looks directly at the camera with a smug smile on his face as he slowly chokes the life out of Mr. Floyd. A public execution by someone who was sworn to serve and protect. Last night people took to the streets and American cities burned. 

Oh America, what has happened to you? There is nothing new, unfortunately and shamefully, about bad cops killing people of color, usually with impunity. To be very clear, these are bad people who happen to be cops, and do not represent the vast majority of police officers. But a number of factors are different in this moment. Everyone carries a cell phone that has a video camera, and the bad cops can no longer lie about the reality of their crime. We are in the middle of a global pandemic, and the United States is number one in the world for the number of cases and deaths from this virus. This pandemic has ripped the veneer off the deep fissures in American society, and many millions of people are in deep trouble. And the President of the United States, Donald J. Trump, is totally incompetent, incapable, and uninterested in being the leader we so desperately need in this time of crisis. We are in a culture war, cheered on by Trump, in which many people have chosen sides: left vs. right, white vs. non-white, native born vs. immigrant, Christian vs. everyone else, capitalist vs. socialist; and the divide has widened to a point where it might not be bridged easily. 

The strange thing about the storm that rolled in this morning was it’s stillness. There was absolutely no air movement; I watched the trees intently and saw no leaf as much as quiver. I stared at the sky and noted the position of the clouds against a fixed point of our building; nothing moved. And yet, the storm rolled in. The lightning was faint and the thunder delayed, meaning the center of the storm was somewhere in the distance. By 6:30 it was raining under a dark sky, and it was eerily quiet. A fitting mood following a disturbing night.

As I write this, savoring the last swallow of coffee from my mug, the sun suddenly breaks through a small hole in the clouds and momentarily blinds me. I still hear rain falling on the deck outside, and our wind chimes are now singing in a breeze. Muffled voices let me know that the radio is on upstairs in our bedroom. Raindrops now glisten on the quivering bamboo leaves outside the kitchen window. Just another Portland morning? No, this one is different.

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WE WENT TO THE PARK TODAY AND HUNDREDS OF PEOPLE TRIED TO KILL US

We are still in the grip of the SARS-CoV-2 pandemic; however, people are now getting out and about. Oregon took the precautionary steps of issuing a stay at home order and closing all non-essential businesses. Now we are cautiously, supposedly, emerging in a planned Phase 1 opening. But there are signs of danger.

Today is a warm, sunny spring Sunday, and here in Portland, Oregon that means people get out. We needed a walk, so we drove to a nearby park, put on our masks, and started down a paved path. There were hundreds of people in the park, many walking, biking, lounging on blankets on the grass, and walking dogs. We estimated that more than 95% of these people were not wearing masks. I think it is OK for people on blankets that are spaced more than 6 ft apart to be mask-less, but it is not OK for people to be walking and cycling and jogging on the paths when there are a lot of other people using them. People like us. 

People like us are the most vulnerable during this pandemic because we are older than 60, and/or have underlying health issues, such as asthma. We were wearing our home-made cotton masks, which protect those around us more than they protect us. We did not feel safe walking in the park on a beautiful day, so we left for the safety of our home. 

Here is the bottom line for me: people need to be more thoughtful and considerate of others. It’s fine if you want to walk around without a mask because you know you will never get this virus (fool that you are); but why do you have so little regard for those around you? You might feel fine, but you can be a carrier of the virus, and you are spewing it in the air space the rest of us share with you. You’re killing us. 

The response in the United States to the novel coronavirus has been dismal and inadequate, which is why we are number one in the world in number of cases and deaths from COvID-19, the disease caused by this virus. Many of the experts keep telling us that we are actually in the early stages of this pandemic, that the virus is not going away any time soon, that we will not have a vaccine any time soon, and that there will be, and already are, increasing outbreaks as we “open up.” We shouldn’t drop our guard, especially now, and we should look out for everyone in our communities. If we had a national strategy that was based on building herd immunity to the virus, and we did it in an intelligent and highly organized way, things would be different. But we don’t have any such strategy. 

Getting ill with COVID-19 is not a walk in the park, but a walk in the park can result in being sick or dying from COVID-19. 

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AND THE DARWIN AWARD GOES TO...THE REPUBLICANS

The Darwin Awards salute the improvement of the human genome by honoring those who accidentally remove themselves from it in a spectacular manner!   https://darwinawards.com/

The Darwin Award is, of course, a tongue-in-cheek honor that many of us laugh about. Usually the award involves someone who does something really stupid and dies because of it, thus removing themselves from the gene pool of humans. But I couldn't help thinking about the Darwin Award as I watched the news this evening.

Elected officials who are Republicans, at every level of government, seem to be purposefully and stupidly ignoring the severity of the novel coronavirus now causing a global pandemic. I don't think they realize that one very real and statistically probable result of their actions is their own death. So I would call this "accidental" in the sense that they are only thinking about partisan politics and not the real outcomes.

Certainly everyone in this country who understands the concepts of protecting ourselves from a deadly virus has seen the President of the United States and the Vice-President of the United States flouncing around without wearing protective masks or socially distancing themselves! The POTUS appears everywhere without a mask. He refuses to wear one. VP Pence violated posted rules at the CDC when he was the only person without a mask. He again appeared without a mask delivering PPE supplies (actually, empty cartons) to a nursing home - a nursing home!  What are these idiots thinking? 

A Republican member of Congress, Steve Scalese, was in a video committee meeting snd launched into a rant about how ridiculous it is that the members of Congress are not in D.C. He touted the fact that he was there, and he was on the video conference from a small conference room at the Capitol. He gleefully walked his laptop around to show the room, a rather small, windowless room, with numerous staff people working in it - and nobody was wearing a mask! "Our entire committee could be meeting in this room right now" Scalese stated, "and everyone would be fine, just like we are." Time will tell how many of those folks end up in the hospital with COVID-19. 

And so I nominate Republicans, including everyone in the Trump administration, members of Congress, governors who are opening their states even though they have not met the CDC criteria, to be the recipients of the 2020 Darwin Award. Homo sapiens will be genetically stronger for it.  

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ET TU, YOUTUBE?

I have been listening to a new podcast titled "Rabbit Hole" by Kevin Roose of the NY Times (see an introduction to the podcast here). To date there are 4 episodes, and I find it very interesting and thought-provoking. Kevin and his team are exploring how the internet changes us, and so far the focus has been on YouTube, using the experience of a single YouTube addict named Caleb. 

I was an early user of YouTube, mostly as a place to put home and work videos and make them available for family, friends and colleagues. After a few years, however, I began to really dislike YouTube, and started using Vimeo for my videos. My biggest issue with YouTube was the "you might like" recommendations and the immediate starting of another video as soon as the one being watched ended. This just felt very intrusive and very annoying. As I listened to Rabbit Hole, the light bulb went off and I remembered my dislike of YouTube, and it now made sense to me. 

I was an early adopter of Facebook, and then joined Twitter when it became popular. Last year I left both of those, and because I never joined Instagram or any of the other "social media" I am now a non-entity on the internet (except for my blog, which you are reading for some strange reason). I am very disappointed with the direction the internet has taken, which is all about profit. And I do not like being surveilled by these giant, obscenely profitable tech companies. I use Signal for texting, and Protonmail for email, and DuckDuckGo for web browsing. This makes me feel like a resister, even though I still have a gmail account, use Amazon, Netflix, Spotify and others that harvest my data and push it back at me as ads. But I look for the rabbit holes, and try to avoid the ones I can.

As detailed in Rabbit Hole, the early and main goal of YouTube was to constantly increase and maximize retention time of users. In other words, capture eyeballs and try not to let them leave the site. It didn't matter what the users were watching, YouTube didn't care about the content, only the retention time. The algorithms build by YouTube pushed content at users based on the prior viewing of each user. It turns out that very large numbers of people are ensnared by this mesmerizing barrage of suggested content and, like Caleb, become addicted. In his case, Caleb at one time spent 12 to 15 hours per day on YouTube. And the algorithm, over time, dragged him to and into a rabbit hole that, in his case, turned him into a far-right extremist white supremacist. Caleb managed to climb back out after a long time down the rabbit hole, but many are not so fortunate.

 

One of the interesting segments of Rabbit Hole is the interviews with Susan Wojcicki, the YouTube CEO. Ms. Wojcicki talked about the early days of YouTube when it's purpose was entertainment, mostly home videos people made of themselves, their pets, and other mostly inane subjects. But YouTube now considers itself to be a media platform that hosts music, gaming, DIY and educational videos in the form of podcasts, informational videos and a variety of other formats.  She talked about recent efforts of YouTube to find and expel the most extreme providers on the platform after YouTube realized that a lot of the platform content was being used for nefarious purposes.  I am happy to learn that YouTube is finally trying to clean up the platform, a very daunting task when you consider the millions of users. 

I still have a problem with YouTube, and I take issue with Ms. Wojcicki about the core of her business; it is still harvesting user data and pushing recommendations made by an algorithm. In my internet searches, I am very often led to YouTube and go there with great trepidation. My basic response is: I do not want your recommendations; I do not want another video to start as the one I'm watching ends; I do not want you to know what I am watching and also harvesting every bit of data from my computer and internet habits that you can glean from my visit. I just want to see the information or entertainment I was looking for. 

The internet is a fabulous technological development, with many positive attributes and uses. That being said, the internet has also become a dangerous place and a technology that giant corporations use to commodify users in order to reap obscene profits. Privacy and security seem not to matter much, only profit. In that regard, we are all down a rabbit hole. 

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WHAT IS A CORONAVIRUS?

It is amazing, from a strictly objective viewpoint, that something as small as a virus can create such havoc in human populations. And from a strictly scientific viewpoint, viruses are fascinating, amazing things. As the 2019-2020 coronavirus pandemic spread across the globe, I began to ask myself numerous questions. What exactly is a virus? Where did they come from and how long have they been around?  What can I learn about their biology? And how is it possible that they can bring human civilization to it's knees?

I’ve taken a very shallow dive into the pool of knowledge about viruses, and this post will be my attempt to provide a hopefully simple summary of what I've learned. A bit wonky, perhaps, but hopefully helpful for those who like wonk. And keep in mind that I am in no way an expert, or even someone with more than a beginning understanding of this science. So take this blog post with a grain of caution that it might not be exactly correct.

As an aside, I had the thought that my quest to understand the viral world is akin to trying to understand the physics of the universe, and that there would be a lot of stuff to read that I would not comprehend. I was correct!

A virus is not a plant or animal or bacterium; in fact, they are not living things, so my wondering about the “biology” of virus is a misnomer. They cannot self-replicate and cannot produce their own energy. So they are things, or agents, and the study of them is chemistry. (Perhaps this is an over-simplification, but I’ll go with it.)

So, let's look at a coronavirus. Basically, it is a tiny bit of genetic material, RNA, inside a capsule. It is called a varian. This particular varian is about 100 nanometers (nm) diameter. A nanometer is one one-billionth of a meter. For scale, the diameter of a human hair is about 70,000 nm, so about 700 of these varians laid side by side would equal the diameter of a human hair. Tiny.

(Figure:https://www.sciencedirect.com/science/article/pii/S0065352706660053#fig0005)

Proteins and lipids and RNA; seems quite simple. The spikes, which make the varian resemble a crown, hence “corona,” interact with receptor proteins in the outer membrane of very specific animal cells. In the case of humans, the spikes activate when they contact cells of the respiratory system, in the throat and lungs; however, recent evidence suggests that this corona virus also attacks other cells, such as kidney, intestine, and maybe others.* Once attached, the varian combines with the human cell, either through fusion or invasion. It then uses the mechanisms of the human cell to replicate the varian RNA and expel new varians. The process is open to mutation, wherein parts of the human RNA get recombined with the varian RNA. The vast majority of these mutations appear to be very minor and harmless, in the context of human disease; however, there are exceptions. This process is shown in the next figure, and if you understand all the notations, explain them to me! Basically, the figure shows a varian attached to a human cell, top left, the processes that occur within the cytoplasm of the cell that replicate the varian RNA, and a new varian being expelled from the cell, top right. 

(Figure source: ibid)

The illness caused by the invasion of this coronavirus is COVID-19 (COrona VIrus Disease 2019). It is typically manifested in three stages in those individuals who get critically ill. It is important to note that, epidemiologically, a large proportion of people who are infected with this virus do not exhibit symptoms and, if they do get ill, have a mild case of the disease.

In Stage 1 of COVID-19, the virus kills the cells it has invaded, and these dead cells slough off and start to clog the lung airways, causing pneumonia. In Stage 2, the body’s immune system rallies to attack the virus and becomes over-active due to the severity of the invasion, and the result is that the immune system starts to kill lung cells. More dead cells are sloughed off, worsening the pneumonia, and as this progresses, it basically eats holes in the lung tissue and scar tissue forms, which stiffens the lungs; this is Stage 3. The result can be respiratory failure, which is why so many critical patients are intubated and put on a ventilator. Changes to lung cell membrane permeability cause the lungs to fill with fluid. As a result of all the above, the lungs can fail to infuse enough oxygen into the patient’s blood, resulting in death.

Sounds pretty gruesome, because it is. 

Where did viruses come from, and when? My surface scratch research suggests that there are several theories about the origins of viruses. One theory is that viruses appeared prior to single-cell life forms, and may or may not be linked to the evolution of living organisms. Another theory posits that viruses appeared within the same time frame as living cells. 

In my simple view, however they originated, viruses developed to take advantage of living organisms by using the organism’s cells to do the work of replication, thereby keeping the varian more “simple” by not needing feeding, reproductive and other systems. I do not think that viruses are simple; they are very complex chemical packets.

Health experts expect this virus to be cycling through the population for more than this cycle. There are some estimates that outbreaks will occur next fall/winter that could be as bad as the current outbreak. In other words, this is not a short-term event. 

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(This post was modified on May 11, 2020 by adding the footnote.)

* There are a lot of unknowns concerning this particular coronavirus, and new information about it is coming out of research labs and groups almost daily. Recent cases have indicated that COVID-19 might be related to strokes in otherwise healthy people in their 30's and 40's. In New York, a number of children who were infected but asymptomatic have developed a mysterious illness, and at least one child has died.