Virus and Vaccines

Copyright © Karl Dahlke, 2023

which kingdom of life contains HIV, the human immunodeficiency virus, the virus that causes aids? Answer: none of them, because a virus isn't alive. If you are aware of this distinction, then you know more science than 99% of Americans.

A virus is a blob of genetic material, DNA or RNA. It has no machinery to eat, metabolize, move about, or replicate. It just sits there like a lump. Your smart phone is more alive than a virus. 📱

These agents of disease evaded detection for centuries, because they are too small to be seen with a lens microscope. A virus is much smaller than a cell, or even the nucleus of a cell. They could not be seen directly until the development of the electron microscope in 1931.

Fast forward to 2020, when we imaged the covid 19 virus and built a 3 dimensional model in a matter of weeks. This facilitated the development of a suite of vaccines, under Trumps Warp Speed Program. Trump said a flurry of absurd and irresponsible things about covid 19, but he also used the power of his office to support medical science, which quelled the pandemic in less than a year. He is rather a contradiction.

If a virus is not alive, how does it cause trouble?

It first enters the body, and then it must enter the cells. This is no small feat. The cell membrane keeps out harmful substances; that is part of its function. But there are openings - channels. The cell must take in nutrients, such as sugar, and expel waste molecules. Certain mechanisms facilitate transport across the cell membrane, and the virus has just the right shape and surface features to trigger these mechanisms. “Open sesame, let me in.”

Once inside the cell, the virus makes its way to the nucleus and hijacks our replication machinery to make copies of itself. We naturally replicate DNA, as part of cell division and other processes. The virus takes advantage of this capability, and thereby multiplies. Copies of the virus exit the cell, the same way they entered, and penetrate neighboring cells, where the replication continues. It is "going viral".

If the virus produces no symptoms in its host, no physiological changes, then it never spreads to another person (or animal). The host eventually dies, and that is the end of the virus. This happens almost all the time, but once in a great while, by accident, a virus induces symptoms, often harmful to the host, which facilitates its spread to others. This is evolution at a microscopic level, survival of the fittest, survival of the virus that multiplies and spreads. The virus may kill its host, or not. It doesn't really matter - as long as it reaches the next host before the first host dies.

Here are some common modes of transmission.

  1. Many viruses employ a form of leakage, various fluids pouring out of the body. Consider the common cold. Your nose runs, and the mucus, laden with virus particles, is bound to reach the mouth or nose of another person. Perhaps you wipe your nose, and mucus gets on your hand, and you touch somebody else's hand, and they raise their hand to their mouth or nose, to scratch an itch perhaps, or to eat some food. That's all it takes.

    If that isn't enough, the virus also causes coughing and sneezing, which sends virus particles flying through the air towards another person.

    The flu causes vomiting, and if the vomit comes in contact with another person, the flu has spread. Even if you clean up the vomit yourself, it's difficult to wash all traces off your hands. Touch a door knob, and the virus remains viable on that surface for several hours, whence somebody else touches the same door knob, and it's a wrap.

    Other viruses cause diarrhea. Again, keeping this fluid contained, without a trace of it touching someone else, is a challenge.

    Citing an extreme example, ebola causes diarrhea, vomiting, and even bleeding. In this case the victim is likely to die, but the virus spreads to others first, so the virus is successful.

  2. When a virus spreads by leakage, it doesn't have to be especially hardy. If it survives for a day outside of the human body, it is likely to enter another host. In contrast, there are some viruses, such as polio, that are extremely hardy. This is because polio spreads from one person's feces to another person's mouth without the benefit of leakage (i.e. diarrhea). This could take a long time, even within the same household, thus the polio virus survives for weeks outside the body. Furthermore, the infected person lives for years, or decades, and remains contagious throughout his entire life. This ensures the spread.

    It seems unlikely, eating somebody else's poop, but it's not. A child often fails to wash his hands after he goes to the bathroom - or he doesn't wash thoroughly, with soap. (Even adults are not always careful.) He reaches into a bag of potato chips, and three days later, his sister reaches into the same bag of chips. She unknowingly ingests a crumb of his fecal matter, and contracts the disease.

    The chlorine in a pool will degrade almost every virus and bacteria, but not polio. In the first half of the 20th century, we documented polio spreading from one person to another, when their only contact was the swimming pool. A crumb of fecal matter would dislodge from the infected person, float around the chlorinated pool for several days, and then enter the mouth of another swimmer. Public pools were closed in an effort to contain the outbreak.

    It's hard to describe the fear that ran through the general public, prior to the polio vaccine in 1955. It's also hard to describe the chronic pain associated with the disease. My grandmother treated polio patients at Shriners hospital. Over several years they lose their ability to walk, and are sometimes confined to wheelchairs, this is generally known, but there is also a tremendous pain in the legs. Gramma would put hot compresses on their legs, in an attempt to ease the pain.

    People would live for years or decades, and gradually lose their ability to walk, and suffer chronic pain for their entire lives, and remain contagious til death do us part. If ever a virus were designed, rather than evolving naturally, then this one was designed by the Devil himself.

  3. Another mode of transmission is sex. this is practically a free ride from one body to another. The virus doesn't have to survive in the outside world at all - not even for an hour. Thus it doesn't have to stand up to environmental stressors. HIV, for example, is particularly fragile. The weak acid in lemonade, or sunlight, will unravel HIV.

  4. The rabies virus is unusual, in that it changes the behavior of the infected animal. It multiplies in the brain, and causes the animal to go mad. The animal then bites other animals, or even a human. The rabies virus passes from the saliva of the infected animal into the body of its new host. From there it can take 3 to 12 weeks to reach the brain, whence the cycle starts anew.

    Once symptoms appear, rabies is almost 100% fatal within a week. Jeanna survived, but they had to keep her in a medically induced coma for 75 days, and after that she had to learn how to walk and talk again. The case made the national news.

    By that measure, rabies is the deadliest virus on earth. We are horrified, but the virus doesn't care. It spreads to another animal before the infected animal dies, and that's all that matters.

It looks like each virus is carefully designed to succeed, perhaps by a malevolent agent, but that is an illusion. For every virus that spreads, there are a million that don't. Perhaps they don't enter the cell, or properly hijack the copier in the cell's nucleus, or exit the cell, or induce any symptoms, or induce symptoms that lead to transmission. Such a virus appears once, by random chance, infects perhaps one person, then disappears. We don't even know it's there. In contrast, a successful virus stays with us for centuries; it may even mutate to become more successful.

The First Vaccine

In terms of killing the masses, small pox is probably the worst virus in human history. It spread across the countryside once or twice a century, and was difficult to avoid. Fatalities could run as high as 30%, even among healthy adults. Sometimes entire villages were wiped out, with no one left to bury the dead.

Throughout the middle ages, the worst insult you could hurl at your enemy was, “A pox upon your house.” We might compare it to wishing cancer on someone today, but cancer is not contagious, whereas small pox could wipe out an entire family.

In 1796, the English doctor Edward Jenner noticed that milkmaids who had gotten cowpox were protected from smallpox. Jenner guessed that exposure to cowpox could be used to protect against smallpox. He was spot on. When it comes to our immune system, forewarned is forearmed. Cow pox was close enough to small pox, that it conferred immunity. That is the very essence of a vaccine. Jenner didn't understand the molecular mechanism, but he knew what he saw.

To test his theory, Dr. Jenner took material from a cowpox sore on milkmaid Sarah Nelmes’ hand and inoculated it into the arm of James Phipps, the 9-year-old son of Jenner’s gardener. Months later, Jenner exposed Phipps several times to variola virus, but Phipps never developed smallpox.

In 1801, Jenner published his treatise On the Origin of the Vaccine Inoculation. (The word vaccine comes from Latin, vacca, meaning a cow.) In this work, he expressed hope that “the annihilation of the smallpox, the most dreadful scourge of the human species, must be the final result of this practice.” Jenner was right, but it took 170 years to get there. Eventually the entire planet was vaccinated, and small pox went away. The vaccine is no longer necessary, and is not part of the cocktail we receive in childhood.

Modern Vaccines

Using a related animal disease, like cow pox, is not a reliable path to building a vaccine, especially since most of our diseases don't have close animal analogues. Instead, we construct vaccines based on the virus itself. We deploy either a weakened version of the virus, that does not cause disease, or a critical piece of the virus, which serves the same purpose as the whole.

Most people receive, during childhood, vaccinations for measles, mumps, and rubella (mmr), diphtheria, tetanus, pertussis (dtp), and polio. Other vaccinations are recommended for teens, adults, and the elderly.


Vaccines can be engineered to protect against bacterial diseases as well, such as tetanus and pneumonia. We will see more of this in the future, as bacteria become resistant to our antibiotics.