Wednesday, January 13, 2021

The Liberation of Light- Technology Quarterly from The Economist

 The January 9-15, 2001 weekly edition of The Economist



This article explains, succinctly, what every introductory science class teaches and tests about the history of light. From Einstein’s simple theories to smart phones, this is a way to understand the theories and equations in narrative form. While we may be good teachers of math and concepts- we may be glossing over big ideas. Big ideas about how politics, personal relationships, and political events shaped the evolution of a scientific discovery. For those of us accustomed to a textbook explanation of history- this is a refreshing read about everything else the textbook leaves out.

Tuesday, November 17, 2020

My front yard

 If you have ever tried to maintain a healthy, green lawn in Southern California you know that it is like pouring water down a long, dry well. It also takes a small bank account to fund the watering of a lawn. Well, its not that bad. But almost. This summer I spent countless hours in my front yard adding extra water to certain spots that were brown. We share our front yard with a neighbor whose property sits behind ours -theirs is the corner lot of our neighborhood. One of the back corners of our front yard is in direct view from their front door- so we try to collaborate efforts on our lawn/front property. I think of the guy next door as the garden guy- he also washes his car a lot in his smooth, long driveway- which he lets us use for rollerblading for my 7 and 9 year olds.

Anyway- turns out the garden guy is the virus guy. I knew he did something in public health but I didn’t realize he was a virus expert. I told him I wanted to learn more about viruses and he went into his house and got me a book. He said, “my student wrote this book.” So- there you have it. My next door neighbor is a virus expert.


This will keep me busy until I get the new vaccine. I have my own expert sitting next door.

Saturday, November 14, 2020

Viruses

“Someday, somewhere, a virus we don’t know about is going to emerge as a major new threat to human health. We’ve seen it happen many times before, and so we know it will happen again. (p74 Planet of Viruses)


Oxford languages definition of a virus: “an infective agent that typically consists of a nucleic acid molecule in a protein coat, is too small to be seen by light microscopy, and is able to multiply only within the living cells of a host.”




As we sit in our houses hiding from a virus, I thought it might be time to learn about viruses. With a degree in basic chemistry the subject of viruses was only on the periphery of my learning. However, the longer the pandemic lasts, the more interested I become in virology and public health. The future of our country seems to depend on it.

Planet of Viruses was written in 2011 by Carl Zimmer and I think there is an update- but on my shelf I have the 2011 edition. This book was written with the University of Nebraska at Lincoln which is the place my parents met in the late 1960s. The entire Kinyoun clan has a large representation of veterinarians, medical doctors and other scientists from this institution- I am revealing my bias right here.

Here is a list of viruses with a short blurb explanation:

Rhinovirus: the common cold. Ten genes each (of the twenty thousand genes in our bodies). This virus lines the cells in our nose, throat, and lungs. In each host cell it makes copies of its genetic material before ripping its host apart and releasing copies of the virus. Because of the mild nature of this virus it may be advantageous to keep it alive in our population for “training” purposes. With it, our immune systems are properly trained in how to manage a virus, albeit a mild one, before coming in contact with something much more virulent.

Influenza Virus: Well duh....what is that? Sorry for the sarcasm. Also just ten genes (like cold virus). Spread from cell to cell in an airway it is like a lawn mower destroying cells and mucus in its way. Originated in birds. Seems to jump between humans, horses, dogs and pigs doing a process called “reassortment” along the way. This means the virus is any given combination of genes from any of these animals at any given time- always fluid and always changing it is impossible to entirely predict which strain will dominate any given year.

Human Papillomavirus: Begins when virus injects its DNA into a host cell, often epithelial cells- skin and mucous membranes. Cell makes HPV proteins from the DNA. The proteins start programming the cell. It duplicates itself. If on epithelial cells, these eventually rise to the top of our skin layer and die off- leaving a fresh layer underneath. Many people live peacefully with HPV for this reason- they are constantly shedding enough virus to keep their system in check. If, for whatever reason, the excess virus is not shed in normal cycle of epithelial growth and regrowth, a tumor forms- and manifests itself as cervical cancer.

Bacteriophages: A possible alternative to antibiotics in fighting bacteria, this is a potential future treatment option in modern medicine. First studied in World War I in soldiers with dysentery, it has only recently been seriously considered as a viable treatment. Viruses may be the solution to antibiotic resistant bacterial infections.

Marine Phages: Outnumber anything else in ocean by 15 to 1. Ninety percent of their genetic makeup is completely unknown to science. The viruses of the ocean exhibit stunning genetic diversity possibly because of the variety of hosts available for infection.

Endogenous Retroviruses: The existence of latent viruses was discovered in chicken DNA. Avian leukosis virus protein was found in healthy chickens. At some point in history, chickens had been infected by the virus and some had survived. These survivors had incorporated the genes for the virus into their genome- the advent of the endogenous or “generated within” virus. At any point, this endogenous virus could reactivate itself and start making chickens sick again. One such virus is responsible for proper attachment of the placenta in the uterus of a human mother.

Human Immunodeficiency Virus: First revealed itself as Acquired Immunodeficiency Syndrome (AIDS). Healthy men with severe pneumonia were mysteriously dying from it- their immune systems were failing. Eventually this was traced to the Human Immunodeficiency Virus (HIV)- a virus that attacks the immune system itself. It has two major forms- HIV-1 and HIV-2. Through genetic sequencing, these two forms have been traced to African primates- specifically sooty mangabeys, which are often kept as pets, and chimpanzees, often killed for meat. Unfortunately, a vaccine for HIV has not been found although a cocktail of drugs can dramatically influence the quality and longevity of life for people who are HIV positive.

West Nile Virus: This virus became a reality for our family when my aunt in Dallas Texas went to the hospital with what she thought was Covid-19 and found out she really had West Nile Virus. Really? You can get infected with West Nile Virus in a Dallas suburban backyard. Not pleasant, to say the least.

This virus emerged in the United States in 1999 although it probably originated in Africa. It seems to exist in many species of birds and is transmitted to other species via mosquito. When mosquitos “bite” humans they inject their saliva into their bloodstream, and with it is the West Nile virus. The dominant strain in the US is most close to that found in birds in Israel in 1998. Somehow these birds found their way to the US- and to the 62 species of mosquitos that have carried them across the US in just four years. In the worst 15% of cases, people develop encephalitis but most people just have fevers, rashes, headaches.

Severe Acute Respiratory Syndrome and Ebola: In 2002 an American businessman developed a fever on a flight back from China and died. It was the first of the SARS epidemic- evolved from the family of corona viruses-originally in Chinese bats. This outbreak of SARS was quickly contained with nine hundred deaths because they were able to track and contain the sources- a catlike animal called a civet was banned from open air markets and people infected were identified and quarantined.

In order to better identify viruses that might make a jump from animal to human there is a team of scientists from a project called the Global Viral Forecasting Initiative. They collect samples in an attempt to better understand exotic viruses and how they might influence global health.

Smallpox: This age-old virus taught modern medicine about vaccines. It infects the airway and causes flu-like symptoms followed by sores filled with pus. It traces back to Egyptian mummies three thousand five hundred years ago. It has wiped out countless civilizations of people. The “prevaccine” method of eradication involved rubbing a scab from a smallpox victim into a scratch of a healthy person. This often prevented the person from getting smallpox- but it wasn’t very reliable. It was rumored that milkmaids never got smallpox and a physician wondered if this was no accident- and it wasn’t. The cowpox illness was passed to most milkmaids and because of the immunity this provided they were protected against smallpox. The process was named “vaccination” after the Latin name of cowpox, Variolae vaccinae.

This is a major argument for better science education- a mere rumor about milkmaids led to a major advancement in western medicine. Think how many advancements would be made if knowledge were more than just a rumor?

Mimivirus: In 1992 a virus in the water of an English town caught the attention of officials looking for the cause of a pneumonia outbreak. They almost missed it because it was one hundred times larger than it was supposed to be. Besides being exponentially larger than expected, it contained proteins that look like proteins in our own human cells. This virus was able to do far more than viruses were thought capable of independently. This raises the question of what is a virus? And more importantly: what does it mean to be alive. According to the definition at the beginning of this post, a virus cannot reproduce independent of its host. For mimivirus, this is not true......Work for the future scientists to investigate this further.

Thanks to this book, and dead time created by the coronavirus of 2020(Covid-19- not the coronavirus of this post) I am much better informed and ready to explain viruses to all of my park friends and their children. Watch out world.

Friday, November 06, 2020

Covid-19: First World and Third World Problems

 



Those of us with first world problems cope with Covid-19 disruptions that include the following:

- Managing children stranded at home while juggling other responsibilities- a husband also working at home (or home due to a layoff), an outside job with its added workload, and housework (which surmounts faster with everyone at home)

-Trying to maintain semblance of health and exercise despite gyms being closed and a lack of general opportunity to participate in organized sports and activities. For most of us this involves heavy use of bicycles and rollerbladers and other first-world outdoor sports gear. (Namely expensive)

-Challenges in maintaining social and relationship connections with heavy emphasis on zoom, drive-by events, social-distance play dates, driveway socializing and other modifications of normal relationship building

So that list really pales compared to this- imagine living somewhere in Africa where Covid-19 is a risk but where malaria is also a risk? In that case, the advice to keep a child at home with a fever can kill the child if the fever turns out to be malarial instead of Covid-19. 

An article in the most recent Economist describes the third-world challenges of Kenya, East Africa. Many people who live in the city believe sending their children to rural areas (with friends or relatives as caregivers) will protect them from Covid-19 and allow them to save money.  After all, fewer mouths to feed is more saved money.

Increased risk of malaria in rural Kenya is the fallacy of parents’ thinking- this is where mosquitos breed in irrigation ditches. Fear of Covid-19 spread hinders distribution of mosquito nets and anti malaria cocktails. There is an attempt at multiple distribution points and alternate pickup times for the mosquito nets but with 15 million Kenyans it is impossible to distribute nets to everyone. 

Then there is the issue of mixed symptoms- is the symptom Covid-19 or is it malaria? If a fever is Covid-19 induced then the patient is advised to stay home. For a fever induced by malaria that would be disastrous, noted Melanie Renshaw, of African Leaders Malaria Alliance. For this reason, all patients with fevers must be tested for malaria. While a portable, quick-prick test does exist- it can only be used once. A resupply is necessary to keep it stocked. And with the disruption of the supply chain this is an obstacle. 

On top of that, the jihad intervene in ways that make it difficult for relief workers to reach the needy population. And many locals already don’t believe in Covid-19- many congregate in crowds, don’t wear masks and generally don’t follow precautions against Covid-19.

As I sit in my suburban living room and read this article, the only part of this story with which I can relate is the pain associated with the malaria disease. I contracted malaria back in 2000 on a two-month trip to Kenya. We were traveling in rural areas with rampant mosquitos and I had been bitten several times. One morning I woke up with the most painful headache. As luck has it- we had traveled to a local medical dispensary for a tour the previous afternoon. The body aches I experienced during my 24-hour illness felt like a knife piercing through my muscles. Walking was difficult because even my bones ached. Fortunately, the medical dispensary was well stocked with a common anti malaria drug that miraculously cured me within 24 hours. Before administering the drug, the doctor in charge made me sign a potential death warrant- the drug itself apparently kills some people. But without it I would face certain death.

There is such a gap between my first-world experience and that described in this article. However, the next time I can’t buy toilet paper at the grocery store, or get frustrated with online, remote learning for my children -I plan to reread the this article and remember third-world problems. If I envision myself writhing in pain with malaria I will welcome an empty toilet paper aisle wholeheartedly. 

Monday, November 02, 2020

Covid-19: did someone actually eat a bat?

“ The emergence of new viral diseases by animal-to-human host switching has been, and will likely continue to be, a major source of new human infectious diseases. A better understanding of the many complex variables that underlie such emergences is of utmost importance to public health.

This concluding sentence from “Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases” published in 2008 in Microbiology and Molecular Biology Reviews is eerily predictive of the emergence of Covid-19 in our world. This article, in particular, addresses the complexity of how a virus jumps from animals to humans. Here is what I have heard from other people about how Covid-19 found its way into the human population:

Fable #1: It came from an open air market where pigs, chickens and other animals are slaughtered and set out for customers to buy. As shown in the movie with Gwenyth Paltrow- Contagion- these markets are not clean and the raw meat is not handled with care. In the movie, it is the chef at a local restaurant that is responsible for handling raw pork before posing for a photo with Gwenyth Paltrow and holding her hand. She later dies from the resulting illness.



Fable #2 Someone ate a bat infected with Covid-19. The virus is thought to have originated in bats so of course it jumped to humans when someone ingested a bat.



Fable #3 It was released from a research lab in China. Someone deliberately injected it into the population to wreak havoc.



None of these ideas is the complete story. The truth is this: the way a virus jumps from the animal population to the human population is not completely understood and likely a lengthy and convoluted process. Three major factors seem to be at stake:


1. How well the receptors on the virus match with the receptors on the recipient animal. In the case of Covid-19, the receptors seem well adapted to enter a human cell which is why the disease has spread so rapidly.



2. Proximity of different animal species to each other. For animals in natural habitats, there is less transfer of viruses due to the lack of opportunity for the viruses from one animal to have any contact with other potentially infectious animals. 

“Fruit bats (genus Pteropus) are the reservoirs of Nipah virus, and planting of fruit orchards around piggeries attracted these bats, allowing spillovers of viruses to pigs and a large-scale outbreak (17), showing how ecological changes brought about by humans can impact disease emergence.”

3. Once a virus has a newly infected host, controlling the spread amongst that new species. “Early detection of inefficiently spreading viruses in a new host would provide opportunities for epidemic control... How viruses gain the ability to spread efficiently is a key question in viral emergence, but the mechanisms involved are poorly understood.”

It seems that when the process is complex and there are multiple unknowns, the resulting information available becomes the notion of fables- wild tales of eating whole bats.


Friday, October 30, 2020

COVID-19 When Doctors Disagree- Controlling the Pandemic

 When Doctors Disagree- Controlling the Pandemic

My angle: Parenting and Covid-



A drive-by event


This article from the latest edition of The Economist brings up a topic discussed at PTA meetings, playground play dates and class “drive-bys.” A new COVID term is a drive-by: an informal party compliant to health guidelines by adhering to a format of “driving by” a predetermined location decked out with a banner, window-painted car and everybody wearing a mask. When people get out of their cars at a drive-by the adults stand far apart and the kids play and everybody hopes nobody says anything about the event escalating to more of a social-distance party.

Should we allow ourselves to achieve herd immunity by not preventing the spread of the disease throughout the population? Or should we maximize suppression of the disease by testing, tracing and isolating those who test positive? The two sides of this discussion are at odds with each other and both are supported by online petitions available for signature. One side of the argument is the Great Barrington Declaration- the side of herd immunity: let the disease take its natural course through the population with extra protection provided for the most vulnerable members of society. The greatest risk in this approach is calculating who is most at risk and successfully isolating and protecting that group. The casualties from this approach mean more short term death and loss. The opposing view is called the John Snow Memorandum named for an epidemiologist in the 1850s: we should take all preventative measures and precautions to protect everybody from Covid-19 at all times. Although more protective in the short term, this could cause longer term loss from the ripples of the economic stagnation.

The PTA and playground version of the aristocratic debate is the following: Should we isolate in our homes and not participate in group play dates, garage social gatherings and drive-by parties (especially when they morph into an event where everybody gets out of the car) or should we relax the rules and gather outside school for birthday parties, play dates and other social events. Should our kids attend school with social distancing implemented, or remain in a remote learning situation? It’s a very real debate amongst parents because the health and education of our children is at stake.

On one hand, I know parents who don’t want to deal with all the turmoil of change. For kids onsite- how long will that last before they are forced to switch back to a completely online model when kids test COVID positive? On the flip side of the turmoil of change is the dullness of staying home- for kids doing just remote learning- how do these kids socialize, get exercise and participate in any organized group activity? This tension has been somewhat relieved most recently by the reopening of playgrounds. Up until a few weeks ago, all social distance and drive-by events took place in large public areas like parking lots and open fields - not public parks. The images in this entry were taken at an event that took place in a large open field available for “passive use.” Technically, people were not supposed to gather on this field- but technically we were a ‘drive by” event where people happened to get out of their cars for a “few minutes.” These few minutes may have been the only few that some of the kids had to socialize with other kids in weeks.

Play dates in people’s houses are another issue. How quarantined are the kids in each household? Do they match in their policy regarding exposure to other people? So far, the consensus seems to be that a play date in someone’s driveway with masks and social distancing is low enough risk that COVID won’t be spread. But this is amongst my social group. And it is usually just two kids.

I know parents who think COVID just needs to take its course through the population and wreak its havoc before it will just go away- the herd immunity philosophy. Those are the people who don’t wear masks, don’t social distance and generally don’t stop the spread of the disease. And they have the freedom to do that- but it makes it harder for families who choose to social distance. It creates two opposing factions of parents- the last thing we all need is more division amongst us.

It’s really an impossible situation- but notable that the argument going on amongst scientists has a PTA manifestation.

Thursday, October 22, 2020

Music during a pandemic and beyond





“ It might seem like a no-brainer that togetherness is a primary benefit of music. But think about that idea in relation to the ways of listening enabled by 20th- and 21st-century technology. When you tune your earbuds to a playlist on a crowded subway, or blast your favorite album alone in your car, what are you doing? You’re regulating your own mood. You’re occupying your mind. You’re enjoying an art form that captures the ineffable. These are great things. But if you’re plugging into a greater human whole, it’s only in a notional way: a feeling of closeness with the singer, perhaps, and with their far-flung fan scene, maybe.”

This quotation taken from an article from Atlantic web page contrasts the traditional ways of experiencing music with the more modern methods of using technology to participate. 

The traditional community centered around a gathering for choir practice, chamber music, orchestra or wind symphony rehearsal  is threatened by the limitations of Covid-19. The traditional community centered around the celebration of a popular singer or rock group suffers from the same. Just as the Internet and home office have eliminated the social interactions of the professional environment, so have ipods, virtual performances and audio-engineered choirs on social media eliminated the requirement of live interactions required for creating and enjoying music. While some of this technology has been available for quite a long time, the increase in sophistication and platform has catapulted its use into making live performances, especially during the pandemic, more atypical than the norm.  We have marginalized the community within the music world- you can create the illusion of the musical experience in a virtual environment and charge money for such events.

One attempt at a substitution for a live performance are the “drive in” performances in empty parking lots. I say substitution because this is still not the same as the acoustics in a performance hall with proper seating and a view of the performers. It is an inferior substitution for a dire situation.



And virtual is never quite the same. My own musical society meets once a month, normally, during the academic year. Since Covid-19 we have resorted to zoom meetings only. Surprisingly, however, this brings some unexpected benefits. The more amateur members of our group (like me) are more likely to volunteer to perform and present slides in a virtual environment. Zoom is more forgiving of subtleties only noticeable at small, live events by sophisticated listeners. In some ways then, virtual meetings open more opportunities for people to participate and build their skills.

But it doesn’t make me any less nostalgic for my season tickets to the San Diego Symphony (given up long ago when I gave birth to my daughter), or my monthly meetings at rotating houses for my music society, informal gatherings of chamber musicians and small local, even free performances all centered around the celebration of music. Not to mention my weekly rehearsals for a local community wind symphony and quarterly concerts at local churches.

The absence of live music is such a hole during this time of isolation. Somewhere in that hole we must find an escape-the drive-in experience or the zoom recital. It is better to create an illusion of connection between people than have none at all.