I BEGAN TO GET INVOLVED IN MICROBIAL EVOLUTION RESEARCH as part of my return to active science in 2010. A wiser me would have realized that an attempt to revolutionize general education was doomed from the start. I soon learned that changing general education is like trying to move a graveyard. At every university, GenEd is associated with strong vested interests in the apportionment of student credit hours between academic units. Thus, in this case I was that voice in the wilderness that those wedded to disciplinary training could or did not want to hear. The UNST program made great strides in improving GenEd at NCATSU, but the program was eventually overthrown by the vested interests who wanted to recover control of the student credit hours associated with the program. In 2010 NCATSU hired a new chancellor, Harold Martin. I was scheduled to meet with him on his first day as chancellor. I expected that I was going to be fired as dean in that meeting and that UNST would be abolished. In the meeting I told Martin that he must decide to either support UNST and provide it with the resources to be successful or abolish it. I also made it clear that I had no vested interest in which decision he made. I felt that my team of faculty and I had done as well as we could under the circumstances, and I was ready to go somewhere else if A&T didn’t need me anymore. I also asked for guarantees that the faculty who were on tenure-track lines in the division would be transferred to the corresponding academic departments of their discipline rather than being let go.

Within a half hour of the meeting I got the call informing me that I was removed as dean of UNST and that the program would be terminated. I wasn’t overly concerned about my own future, as several other universities were already recruiting me to take the reins of similar programs. However, within the hour I received a call from NCATSU’s dean of engineering inviting me to take up a full professorship in that college. I explained I wasn’t an engineer but said I would think about it. A few moments later I received a call from James Ryan, the dean of the newly formed Joint School of Nanoscience and Nanoengineering (JSNN). JSNN was a partnership between NCATSU and the University of North Carolina, Greensboro (UNCG). Ryan wanted me to take up the post of associate dean for research. I explained to him, too, “Jim, I don’t know anything about nano.” He didn’t care. He wanted someone who could be a role model for his junior faculty in how one sets up an externally funded successful research program. I told him I could do that and accepted the post. I requested a year to retrain myself in research. He agreed.

I wrote a retraining grant proposal for senior faculty and submitted it to the NIH. The proposal was designed to allow me to go to the National Evolutionary Synthesis Center (NESCent) for a year and retool in computational biology working with its director, Allen Rodrigo. The year I spent at NESCent was outstanding. My office mate was Dave Swofford (designer of the phylogenetic software PHYLIP). He helped me a great deal in learning how to run phylogenetic analyses. I also took two summer courses. One was on general computing in biology and was organized around Steven Haddock and Casey Dunn’s book Practical Computing for Biologists.¹ The other was on next-generation sequencing (NGS) data analysis at the Kellogg Biological Station at Michigan State University (MSU) taught by Travis Brown (now at the University of California, Davis). During my time at NESCent and Kellogg I had the opportunity to work with some outstanding young scientists who were then postdoctoral researchers or graduate students and who ended up collaborating with me on research (Kate Hertweck, Mira Han, and Mark Phillips).

While I was at NESCent, I thought about what kind of research program I could set up in the new JSNN building.² The building was designed to be a state-of-the-art nanofabrication and nanocharacterization facility. It was clear to me that I wasn’t going to be able to set up a fruit fly colony in the building—the users of the clean room would not have been happy about fruit flies getting in their projects. However, there was an important problem developing concerning the use of nanomaterials as antimicrobials. Nanomaterials were thought to be useful in this regard because materials take on new (and unanticipated) properties on the nanoscale (any dimension on the order of 10⁻⁸ m, or around 1 nm). Research was already being published claiming that silver nanoparticles would be the new magic bullet to control multidrug-resistant (MDR) bacteria. Silver was proposed because it affected so many aspects of bacterial physiology at the same time. Thus, the reasoning went, the evolution of resistance would be more difficult because mutations would be needed in so many different systems at the same time.³

Despite the fact that I was not yet a microbiologist, I read these reports with great skepticism. Ian Malcolm’s words rang in the back of my mind: “Nature always finds a way.” My first paper on the subject, entitled “A Grain of Salt,” outlined all the reasons why the magic bullet claim was probably not true.⁴ Chief among my objections was the presence of silver-resistant genetic elements in various microbes in nature, the widespread existence of silver resistance in bacteria isolated from burn wards, and the history of rapid evolution of resistance to antibiotics. However, theoretical objections are not in themselves enough to change people’s minds. Therefore I designed a simple experiment to determine if a naive bacterium (Escherichia coli) could evolve resistance to silver nanoparticles. I also chose to use the experimental evolution protocols utilized by Richard Lenski to test this question. The experiment was in part facilitated by NSF funding from the Science and Technology Center (STC) entitled Biocomputational Evolution in Action (BEACON).⁵

We began the experiment in the summer of 2014. Via BEACON support, my research group included URM students from both NCATSU and MSU. I had also taken on the direct mentorship of Mehrdad Tajkarimi (a graduate student in the UNCG Nanoscience Department). Mehrdad had had a great deal of experience in industrial microbiology before he entered the PhD program in nanoscience. He was responsible for setting up the experiment and providing the undergraduate students with hands-on wet-laboratory training. I provided everyone in the research group with the overarching principles of microbial evolution (tiered mentorship in action).

I was not surprised when we found that E. coli was capable of evolving resistance to silver nanoparticles (AgNPs) within thirty-seven days.⁶ In addition to finding that the evolution of AgNP resistance was rapid, we showed that its genomic foundations were simple. The effect resulted from mutations in the gene cusS, a protein that is normally part of a response system that senses the levels of both silver and copper in the cell. In addition, we observed mutations in the ompR gene that encodes OmpR, an outer-membrane protein. Finally, one of the most intriguing mutations we found was in the gene rpoB, responsible for producing one of the subunits of the enzyme RNA polymerase. RNA polymerase is responsible for putting together all the RNAs that a cell makes, thus in turn potentially influencing every protein the cell makes. These kinds of mutations are pleiotropic, meaning that one gene affects multiple physical traits (a phenomenon that had played an important role in my earlier research on aging in fruit flies; see Chapter 4). The resulting paper was published in Frontiers in Genetics and in April 2015 was featured on the journal’s home page, a recognition due to the fact that we were the first research group in the world to report rapid evolution of AgNP resistance in bacteria.

We soon followed that experiment with a larger study examining E. coli’s capacity to evolve resistance to ionic silver. This experiment logically followed from the fact that the mechanism of AgNP toxicity to bacteria was the release of silver ions. Experiments exposing bacteria to AgNPs in an environment without oxygen had already shown that they had no effect on the bacteria; under those conditions silver does not form ions. The results of the experimental evolution against silver ions were similar to what we had found with AgNPs. The evolution of resistance was rapid, and resistance to silver ions conferred resistance to AgNPs. The genomic foundations were similar (mutations in cusS, ompR, rpoB, and rpoC; the gene rpoC encodes the c subunit of the protein RNA polymerase).

There was also striking parallelism in the specific mutation in the cusS gene that we found in this study. We started with twenty independently founded populations chosen from twenty randomly picked colonies from the ancestor E. coli strain. Of the thirteen that showed a mutation in the cusS gene, eleven shared the exact same mutation, R15L—that is, at the fifteenth amino acid of the protein, arginine was switched out and replaced with lysine. Both amino acids carry a positive charge, but arginine has three NH groups (nitrogen bonded to hydrogen), to only one for lysine. The charge structure of amino acids matters because the function of the proteins they form is determined by their three-dimensional structure. The change in the amino acid at position fifteen occurred because at position 594,727 of the E. coli genome in these populations, a guanine (G) was switched to a thymine (T) nucleotide. The amino acid sequence produced by a DNA chain is determined by a triplet code (that is, three of the nucleotide letters—A, T, C, G—in a row code for a specific amino acid). With three positions and four nucleotides, the code can specify 4³ (= 64) amino acids. In living things on this planet, there are twenty-three naturally occurring amino acids, so the code is redundant. A nucleotide change resulting in the spelling of a different amino acid is called a nonsynonymous nucleotide change (meaning that a new amino acid results in the position). Synonymous changes in the triplet code spell out the same amino acid.

The parallel appearance of the R15L mutation in eleven of the thirteen populations was not accidental. We first considered the possibility of a simple contamination event in the daily transferring of populations to fresh medium. However, if that had happened, the different populations would have shown the same mutational profiles for all the mutations we observed, not just one. We did not observe that, which suggested that there was something special about the R15L substitution, that it was better at sensing silver than the other three cusS mutations we found (T14P, L12R, and N279R). We also noted that three of the four mutations in the silver-resistant populations were in the sensory domain of the protein. My colleagues Kristen Rhinehardt and Misty Thomas utilized molecular-modeling software to show that it was highly likely that the R15L structure of cusS did in fact bind silver ions better than the other mutations. However, the final test involved placing the different mutations on a plasmid (a small piece of circular DNA), inserting them in another E. coli strain, and demonstrating which of them produced the best silver resistance. Once again, R15L came out in first place. These results were promising enough to spur a research grant that is studying the role this response system plays in allowing bacterial adaptation to silver. The NSF funded the project so that Thomas, her students (all African American women, by the way), and I are currently working on this project.

The significance of our findings concerning silver did not cause immediate ripples in the materials-science world. However, within a year the citations of the 2015 paper in Frontiers of Genetics began to skyrocket. In the summer of 2017 I was attending the meeting of the International Society for Evolution, Medicine, and Public Health (ISEMPH) in Groningen, Netherlands. During one of the breaks I noticed that the citation manager on my phone had gone off. (Citation-manager software alerts you when someone has cited your research in a journal paper.) Usually I am quite happy when someone cites my work, but when I read the abstract of the paper citing mine (published in the journal Nanomaterials), it became quite clear that the authors really did not understand our work and were using it to incorrectly support their results. On the plane ride home I began to outline my response to their improper citation. It was important that I write a piece that would illustrate, for a broader audience than these researchers had addressed, why much of the antimicrobial materials research was improperly formulated. At my office the following day, I outlined for my then closest colleagues, Misty Thomas and my postdoctoral researcher, Jude Ewunkem, the need for the piece. I then sat down at my word processor, and approximately thirty-two minutes later I had the first draft of the paper. (I was quite pleased with myself, because I had a running competition going with Michael Rose as to who could write a first draft for publication in a science journal in the least amount of time. Prior to this Michael held the lead in our competition at forty-eight minutes.) The paper was reviewed by Thomas and Ewunkem, comments were made, and then I submitted the paper via the online submission portal to Nanomaterials.⁷

From 2016 to 2021 my group continued to publish important studies on how bacteria evolved resistance to various types of ionic and nanomaterial metals.⁸ This work convinced me that a book-length treatment of the problem was necessary. After a discussion with a subject editor at Elsevier, I embarked on writing a full-length discussion of antimicrobial materials. The book was completed in December 2020, at around the same time I completed a book on race and racism with my coauthor Alan Goodman (a former president of the American Anthropological Association). Both books were published in the fall of 2021.⁹ Undoubtedly, the SARS-Cov-2 pandemic played a role in my fierce dedication to get both of these books finished in 2020. Going into the pandemic, I honestly didn’t think I would see the other side. Obviously, I did survive that first phase. However, with first the Delta variant and then the Omicron variant sweeping the country among the unvaccinated, the breakthrough cases among the vaccinated, and the dropping efficacy of the available vaccines, who knows how long any of us will survive.

“(DON’T FEAR) THE REAPER” (FROM BLUE ÖYSTER CULT, RELEASED in 1976) plays during the lead-in to the 1994 made-for-television miniseries version of Stephen King’s iconic novel The Stand. King is my favorite fiction writer, and I enjoyed this more than any of his other books. Good fiction needs a plausible plot as well as strong characters. King gives you all that in The Stand. To give the plot in brief: Supernatural forces collude to release an engineered flu strain (nicknamed “Captain Trips”). Initially the US government denies the existence of the superflu, but it soon realizes that the mutation that made it less lethal but more transmissible cannot be contained. In the unabridged version of the novel, published in 1990, the US government decides to use the flu in a strategy of “mutually assured destruction” against other nations. It sends people carrying the virus on jets to all the major cities of the world to guarantee its global spread. Within weeks, 99.9 percent of the world’s population is dead. Then the real drama begins (but I’m not going to spoil it for you). CBS All Access (now Paramount+) couldn’t have known that their release in 2020 of a second miniseries version of The Stand would air during a worldwide pandemic. It’s hard to know whether the second miniseries received a lower audience score because people didn’t want to watch a pandemic during a pandemic, or just because the new version deviated so much from the novel that (I felt) it was almost a new story.¹⁰

The reason The Stand originally worked so well as a novel is that plagues caused by microbial organisms have been with us throughout our recorded history. It is important to distinguish plagues from endemic diseases. For example, malaria caused by the eukaryote sporozoans of the genus Plasmodium (e.g., P. falciparum, the killer, and P. vivax, a milder species) has probably been with us since humans invented agriculture and domesticated animals.¹¹ Another endemic disease, schistosomiasis, was the focus of my master’s degree research. Plagues are more properly thought of as episodic infectious diseases that are initiated by an “outbreak” event, spread somewhat rapidly, make sick or kill many people, and eventually taper off. Viruses and bacteria are the usual cause of these outbreaks. Remember that viruses are noncellular life that must be obligate parasites. They differ from bacteria in that they require a host cell to replicate their genetic codes.

Many people are familiar with the Hebrew Bible (Old Testament) account of the ten plagues that God sent against Egypt. Modern analysis suggests that the first nine of these can be accounted for by natural and reoccurring phenomena of the Nile Valley.¹² The bloody appearance of the water (called red tide) and the fish kills happen routinely as a result of algal blooms of dinoflagellates. The prophet Samuel describes what was probably an outbreak of bubonic plague (caused by the bacterium Yersinia pestis) among the Philistines around the year 1320 BCE. The Chinese described an outbreak of smallpox that spread to Korea and Japan in around 49 CE. Even worse was the Antonine plague of 165–180 CE that might have killed upward of five million people. It probably began in Iraq and was passed to the Germanic peoples, who passed it to the Romans.¹³ The effects of the black (bubonic) plague are well-known. It probably began in central Asia, but it spread to all of Europe and the Middle East over a five-hundred-year run, beginning around 1346 CE. The plague had largely abated by 1600, but it reduced the European population almost by half, and mortality ranged from 25 to 70 percent of those infected.

Plagues have been an ongoing feature of human existence. To understand why, a reference to both ecological and evolutionary theory is useful. As a young ecologist (before I got wise and switched to experimental evolution) I marveled at both the deep insight and the compelling writing in G. Evelyn Hutchinson’s essay “Homage to Santa Rosalia, or Why Are There So Many Kinds of Animals?”¹⁴ Hutchinson reasoned that the number of plants and animals was determined by the various ways through which organisms could “make a living.” He relied on the idea of the “niche,” that is, where an organism fits in the myriad interactions of ecological communities. The niche describes what the organism does, as well as what is done to it. He proposed that various species cannot occupy the same niche, as natural selection will always drive species behaviors and characteristics apart. However, Hutchinson’s discussion stopped short of the mark. Like so much of the biology of the late nineteenth and mid-twentieth centuries, it generated its ideas from observation of macroscopic organisms such as animals, fungi, and plants. However, these species are only the tip of the iceberg.

This is a microbial world, always has been and always will be. The sheer immensity of the microbial world is staggering. It is estimated that there are over one billion species of bacteria, comprising over 10³⁰ (1 with thirty 0s after it) cells! There are even more viruses; there are over ten million bacteriophages (viruses that attack bacteria) per milliliter of sea water.¹⁵ We really have no good estimate of how many “species” of bacteriophages there are, but it is likely that several bacteriophages can attack each bacterial species, so there must be more species of phages than there are of bacteria. To put these numbers in perspective: it is estimated that the grains of sand on earth and stars in the known universe both number about 10²¹. That means that there are fewer stars in the known universe than there are bacteria on this planet! If that doesn’t make your head spin, consider this: I did a back-of-the-envelope calculation of the number of COVID particles circulating in the United States during the pandemic on January 4, 2021. One study found that the average patient who died from COVID had 1.34 × 10¹¹ (= 134 billion) viruses per milliliter (ml) of blood.¹⁶ A person weighing between 150 and 180 pounds has about 1.5 gallons of blood, or 4,500 ml. On that date, the number of known infected Americans was 20,558,489 persons. I multiplied those numbers and got at least 1.24 × 10²² SARS-CoV-2 viruses in the United States on that day—again, more coronavirus particles than stars in the known universe!

Why so many microbes? The answer is somewhat simple. There are many more ways for these organisms to generate energy for their growth and replication than there are for large-bodied organisms. Unfortunately for us, we are one of the ways microbes such as viruses, bacteria, fungi, and parasitic eukaryotes make their living. However, let’s not forget that bacteria also make it possible for us to exist. They run key aspects of biogeochemical cycles, such as for the elements carbon, nitrogen, sulfur, and phosphorous. This means that bacteria facilitate the movement of these elements from the atmosphere, soil, water, sediments, and other reservoirs, making the biosphere possible. Microbial communities, such as those that inhabit our skin, gut, respiratory tract, and for females, vagina, are also essential parts of our bodies.¹⁷ There is a growing body of evidence that dysregulation of human microbiomes is associated with a variety of diseases, such as metabolic disorders and mental illness. Also, it is likely that the phage community of our gut plays a role in regulating the types of bacteria that live there.¹⁸

On the other hand, large-bodied, structurally complex organisms such as ourselves could not exist without an evolved combination of innate and active immunity. Our lymphocyte cells use a combination of somatic recombination and mutation to generate the diverse antigen receptors required to keep up with the rapid evolution of the pathogens that attack us. It might amaze you to know that a transposase gene (a gene that makes the enzyme that allows transposable genetic elements [TGEs] to change their places in genome) is required for the alteration of a somatic cell’s DNA in the adaptive immune system. This gene was inserted by a TGE in the ancestor of the jawed fishes (about 500 million years ago). The genes RAG1 and RAG2 are recombination-activating genes. We now know that mutations in these genes are one cause of the disease called severe combined immune deficiency (SCID). The prevalence of this disease worldwide is only about 1 per 1,000,000, because people who cannot protect themselves from microbial infection usually die before they reach reproductive age. Population-genetic theory predicts that the frequency of such genes will be determined by how bad they are, balanced by the rate at which the gene reappears as a result of mutation (mutation/selection balance).¹⁹ However, in the Navajo and Apache Nations, the frequency of this terrible disease is 1 per 2,000.

Why is the frequency so high in these nations? It is the result of the drastic reduction in the size of these nations due to the violent seizure of their land by European Americans.²⁰ From 1863 to 1868, the Navajo population was interned at Fort Defiance in what is now Arizona, from which they made multiple treks of 250–400 miles (depending on the route), including the Long Walk, to Fort Sumner in New Mexico Territory.²¹ Approximately 10,000 Navajo began the journey, but many died on the way or at the New Mexican camp.²² It is thought that about 8,000 survived. From that small population, the Navajo now number about 330,000. The Jicarilla Apache declined to a population of approximately 600 in the early twentieth century and now number about 3,300.²³ This drastic alteration of gene (allele) frequency due to catastrophic reduction of population size is called genetic drift. Genetic drift is a random process. Sometimes bad genes jump to high prevalence, increasing to levels that could never have been reached by natural selection due to bad luck. The high prevalence of SCID among the Navajo and Apache Nations is one of the long-lasting impacts of genocide. Another example of this is the high prevalence of the BRCA1 and BRCA2 (breast cancer) mutations in those Ashkenazim (persons of central- or eastern-European Jewish descent) whose parents and grandparents survived the Nazi genocide in World War II.

VIRAL EPIDEMICS AND PANDEMICS HAVE BEEN WITH US A LONG time. Their rise in prevalence is related to the transition from a hunter/gatherer lifestyle to a sedentary, agriculture-based life, which occurred around ten thousand years ago. Prior to this, the human population worldwide could not have been more than about ten million people.²⁴ The transition to agriculture was responsible for increasing both size and density in human populations, yet still, by the first century CE, the entire world’s population was no more than four hundred million. It was the Industrial Revolution that really got human population growth going; by 1850 the world’s population exceeded 1.3 billion. With adequate resources, the world’s population will continue growing, and as it grows, given the power of exponential growth, the doubling time gets progressively shorter.

The population density of hosts is important because viruses cannot move on their own. They require other organisms to transmit them. The more densely populated humans are, the greater the ease of transmission. Direct methods of viral transmission include animal bites (rabies), sex (HIV), and sneezing (coronaviruses). Indirect methods include water, insects (yellow fever), and blood (HIV). The transmissibility of a virus is called its R-nought (R₀) number, which indicates the number of secondary infections expected to occur in susceptible people caused by one person carrying the virus. For measles, the R₀ is 12–18; that is, one person with measles can be expected to infect from twelve to eighteen other people.²⁵ A simple familiarity with exponential growth demonstrates how bad a viral pandemic could get with an R₀ of 12. One person could literally lead to infection of every person in the world in a couple of viral generations. If the R₀ is less than 1.0, then the viral infection should die out. The initial conquest of New England by Europeans was facilitated by the smallpox virus (Variola major). Just before the landing of the Mayflower in 1620, smallpox had spread from English trading ships to the Amerindians of the region, who were thus in no position to resist the establishment of Plymouth Colony by the English.²⁶ The negative impacts on the Amerindian populations of viral and bacterial diseases brought by Europeans were facilitated by the lower genetic variability of the former compared to the latter. Amerindian peoples were descended from smaller populations originating in Eurasia, so the genetic variability of their HLA loci (histocompatibility genes, which help the immune system recognize foreign proteins and carbohydrates) was greatly reduced, making them more susceptible to novel microbial diseases.²⁷ It is likely that more Amerindians died from the combination of new epidemics and the disruption of their ecology than from the direct warfare conducted against them during European colonization.

The disparity between the genetic variability of the Amerindian nations and the greater genetic variability of the novel pathogens they encountered is also explained by the Red Queen hypothesis (see Chapter 10). In this case, the Red Queen analogy proposes that there is a constant evolutionary arms race between pathogens that wish to infect a host and the host’s capacity to resist infection. Sexual recombination plays a large role in maintaining the diversity of hosts to be defended and of eukaryotic parasites to attack them. Amerindian populations lost much of their genetic variation during their migration to North America from Eurasia. They did not have sufficient time to recover that variation before European colonization brought new pathogens for which they had no active immunity. An additional problem for large-bodied and relatively long-lived organisms, such as ourselves, is that viruses, bacteria, and eukaryotic parasites evolve much more rapidly than we do. The descendants of an organism that evolved active immunity deal with parasites’ faster evolution via their ability to detect foreign proteins and carbohydrates in their bodies, particularly certain large molecules (such as lipopolysaccharides and peptidoglycans) that are retained by microbial pathogens across their evolution. The key players in our immunity are the T and B lymphocytes (that is, T-cells, which are produced by the thymus gland, and B-cells, which are produced by the gut). The T-cell receptor patterns are produced by a combination of somatic recombination, gene conversion, and random pairing of receptor units, which together can recognize virtually any antigen. Some of the T and B lymphocytes have a long-term memory that allows them to store information concerning common pathogens. This capacity is the basis of vaccination.²⁸

In 1917 a novel influenza strain (H1N1) surfaced; humans had never been exposed to it. This strain probably resulted from a recombination of bird and pig variants. Though it was called the Spanish flu, it is more likely that this variant originated in the United States.²⁹ It is highly likely that it was passed to Europe by American soldiers sent to participate in World War I. The tragedy here is that American army doctors began to realize there was a serious problem brewing with this new infectious disease. The infection was sweeping through army bases, where men were living in close quarters. Army doctors such as William Henry Welch and Army Surgeon General William Gorgas objected to keeping men in close quarters and moving sick men from base to base. Their greatest fear was that an epidemic would break out among the troops and spread to the civilian population. However, the Wilson administration, in its fervor to get Americans into the fighting in Europe, largely ignored the concerns of the physicians.³⁰ The result was the dramatic spread of H1N1 influenza across the United States, Europe, and then the rest of the world.

The 1916–1917 flu variants tended to be most lethal to very young or very old individuals (particularly for those over sixty-five). However, by 1918 the variants had evolved to be more lethal, with patients dying very quickly, a day or even less after the appearance of symptoms. They probably died of an overwhelming and massive invasion of the virus in their lungs. The combination of the virus’s destruction of enough cells in the lungs to block the exchange of oxygen and the body’s own inflammatory response against the virus resulted in the patient’s death. But more important, the 1918 variants killed across age categories, indicating that the virus had evolved greater virulence.³¹ Virulence is defined as the capacity of the parasite (virus, bacterium, etc.) to inflict damage and reduce the host’s evolutionary fitness. This can occur by several means: reduction in host fecundity, increase in host mortality, reduction in host body condition, and tissue damage. However, virulence may not be an adaptive trait for the parasite; it may result from unselected side effects—mistakes—during the infection, side effects that are detrimental to both parasite and host. The side effects could result from the way the parasite extracts resources from the host or from the way the host responds to the infection. Immunopathological effects by which the host response itself causes the damage results in selection on the host to mediate the response mechanism, but it does not lead to selection on the parasite.³²

A parasite can evolve to become more or less virulent. In 1950 the Myxoma virus was collected from rabbit populations in Europe and used to control an outbreak of rabbit populations in Australia. In following years the Myxoma viruses evolved to be less virulent. This experiment showed that viral clones evolved less virulence, and the rabbits evolved more resistance. We have observed that generally, when parasites are introduced to a new host, they tend to be more virulent. This was the case with the Ebola fever, Lassa fever, SARS, and now COVID-19 in humans. On the other hand, infections with a long evolutionary history in the host tend to be less virulent.

With these facts in mind, relatively early on in the coronavirus pandemic (February or March 2020), I attempted to warn the public about the danger that SARS-CoV-2 would evolve either greater transmissibility or greater virulence.³³ There were very few of us issuing these warnings at that point. The Trump administration did not want this message heard, as they were still downplaying the seriousness of Coronavirus 2019. Indeed, their lack of a coordinated national plan to contain the virus cost hundreds of thousands of lives. In addition, the ongoing high numbers of infected people across the world has allowed the evolution of new and more dangerous variants, such as Delta and Omicron.³⁴ Recall the calculation I did above of how many SARS-CoV-2 viruses were circulating in the United States on January 4, 2021—at least 1.24 × 10²². But that number is an underestimate, because it only included people with confirmed cases, not those who may have been infected with the virus but were not showing severe symptoms.

We must do more than control the cases in the United States. As cases dropped here in June 2021, they rose in Mexico.³⁵ If Mexico’s transmission of the virus is not controlled, it could easily become a reservoir of infection that will spread into the United States. The ongoing dynamics of SARS-CoV-2 transmission has put millions of lives at risk. The Delta variant arose somewhere in India in late 2020 and by summer of 2021 had swept the world, accounting for over 90 percent of US COVID infections by August 2021.³⁶ This unfortunate situation was entirely avoidable in the United States, as the summer 2021 surge of COVID-19 infections was driven by unvaccinated persons. In the main, these individuals were eligible to be vaccinated but chose not to be, and much of their resistance to vaccination was the result of individual political affiliation rather than for medical reasons. Of course this ideology plays into the hands of the parasite, as the unvaccinated represent a reservoir in which the SARS-CoV-2 virus will further evolve its capacity to infect humans (across all age classes).

In the summer of 2021, prior to the emergence of the Delta variant, the CDC allowed relaxation of masking guidelines across the country. They reasoned that vaccinated people are less likely to transmit SARS-CoV-2 and that vaccinated people who do contract the virus are less likely to become seriously ill.³⁷ The flaw in their reasoning was that not enough Americans (or persons in other nations) were vaccinated. Even worse, projections at the time suggested that the United States might never reach even 80 percent vaccination among adults. As of August 21, 2021, the average number of adults vaccinated in the United States by state was 53.0 percent; the District of Columbia led the way, with over 72 percent vaccinated, and Mississippi, Alabama, and Wyoming were on the low end, with vaccination rates in the mid-40s percent range. As of February 11, 2022, the national average for fully vaccinated persons by state was 65.02 percent. The District of Columbia was still highest at 89.78 percent. There were twenty-three states above the average. The states with the lowest vaccination rates were dominated by those that Donald Trump won in 2020 (with the exception of Georgia). Wyoming and Alabama had the lowest vaccination rates, at 49.95 percent and 50.04 percent, respectively.³⁸ Unfortunately, resistance to vaccination against COVID is more reflective of political ideology than of scientific fact. On May 14, 2021, CNN reported that the majority of Republicans in the House of Representatives would not confirm whether they had received a vaccination against SARS-CoV-2.³⁹ On August 31, CNN reported that there was a direct correlation between being not vaccinated and listening to right-wing news outlets, after three leading conservative broadcasters died of COVID.⁴⁰

In that same month, I again issued a dire prediction for the world if the situation were to continue.⁴¹ In short, I stated that if we did not get more people in the United States and in the world vaccinated, we could be soon be facing a crippling pandemic on the order of the one in 1918, which cost the lives of hundreds of millions of people. So far this has not happened, so that is good news. However, with the Omicron variant transmission beginning to recede in the early months of 2022, several states are already lifting their mask requirements. It is my fervent hope that by the time you read this, reason will have won the day and we will see nationwide adoption of mass vaccinations, mask mandates, and social distancing in public spaces.

IT IS TOO EARLY TO PREDICT HOW SARS-COV-2 WILL EVOLVE. So far, we have seen the emergence of variants that are both highly transmissible and also cause greater illness (such as Delta, which has an R₀ of 9). Worse is that the efficacy of both the Pfizer and Moderna vaccines have dropped by about 25 percent against Delta, which in the middle portion of 2021 accounted for more than 98 percent of current infections.⁴² However, the Omicron variant was first reported in late November 2021. It spread like wildfire among the unvaccinated because it was more transmissible than the Delta variant (although suspected to be less virulent). By December 25, 2021, it accounted for more than 70 percent of US cases, and by January 29, 2022, it had completely replaced the Delta variant among new cases of COVID-19.⁴³ Again, I hope that it will move toward greater transmissibility at the expense of virulence, eventually ending up like influenza. This would mean that our SARS-CoV-2 immunization would become a yearly ritual, but it would still mean that older people or those with preexisting conditions or compromised immunity could die from it. Given the number of people infected worldwide and the low level of vaccination, it is still possible for SARS-CoV-2 to go the route of the 1918 influenza that killed people across all age groups and conditions.

However, as viruses go, SARS-CoV-2 is not the worse villain we could potentially face. Other viruses of continued concern are influenza viruses, dengue virus, the virus that causes MERS (Middle East respiratory syndrome, also a coronavirus), Rotavirus A, Zika virus, and Ebola virus.⁴⁴ Ebola is one of twelve described filoviruses, of which seven have been found in humans. Ebola disease (acute hemorrhagic fever) is caused by four of them. Ebola viruses are negative single-stranded RNA viruses. Their genome has about nineteen thousand base pairs and a high mutation rate: about 1.3 × 10⁻³ (or 1.3 per 1,000) per base pair per generation. This is among the highest mutation rates ever observed; by comparison, the mutation rate of double-stranded RNA viruses, such as HIV and the coronaviruses, is about 1 in 100,000 to 1 in 10,000; of bacteria, about 1 in 10 billion to 1 in 1 billion; and of humans, about 1 in 10 million.

The first recorded outbreak of Ebola virus disease was in Zaire (now the Democratic Republic of the Congo) in 1976. There were 318 cases, with an 88.1 percent fatality rate. Since then there have been nineteen major outbreaks, most originating in equatorial Africa. The most important cautionary tale of Ebola disease was the 2013–2016 outbreak, which reached the United States, France, Germany, Netherlands, and Norway. That outbreak had 28,652 cases; its fatality rate was only 39.5 percent.⁴⁵ It is possible that the lower fatality rate (virulence) of that variant came as a trade-off for higher transmissibility, a possibility supported by some evidence from sequence data. That outbreak was one of the first in which next-generation sequencing (NGS) methods were able to track the evolution of the virus’s genome within days and hours of taking patient samples. About 5 percent of all patients during the outbreak had their Ebola variants sequenced.⁴⁶ So far, we haven’t achieved that level of sequencing for SARS-CoV-2, for which around 1 to 3 percent of patients have been sequenced. You can observe the ongoing evolution of COVID at the Global Initiative on Sharing Avian Influenza Data (GISAID) website.⁴⁷

HUMANS ARE NOW VICTIMS OF THEIR TECHNOLOGICAL SUCCESSES. Unfortunately, our ethical and moral development has not kept pace. This contradiction is what makes us perfect fuel for viral and bacterial pandemics. Our population, at more than 7.8 billion individuals, now exceeds that of any large-bodied mammal in the history of life on this planet. You can watch our population grow in real time at the World Population Clock.⁴⁸ But we are not distributed randomly over the habitable land on the planet. We are concentrated in cities and suburbs. Even within these urban environments, we are not distributed randomly. In most of the world, the wealthy inhabit less crowded and more comfortable lodgings than the poor, who are more likely to be concentrated in ghettoes and slums. In the underdeveloped world, the homes in ghettoes and slums are often made of cardboard with tin roofs and the neighborhoods lack plumbing and sewers. In the industrialized world, the wealthy enjoy well-constructed, adequately distanced homes, close to green spaces, with many fewer persons per household; they enjoy cleaner air, ample automobile transportation, and access to grocery stores. The poor are packed into ghettoes and slums, with less access to green spaces, with many more people per household; they have fewer grocery stores and must rely on mass transportation.

The methods we use to maintain these high and densely packed populations help breed MDR microbes (viruses, bacteria, parasitic eukaryotes). In my 2021 book Antimicrobial Nanomaterials I spent a great deal of time showing how these conditions accelerate the evolution of multidrug resistance. The largest use of antibiotics across the world is not to heal humans of infectious disease but, rather, to keep industrially farmed animals “healthy” and to promote their growth. The runoff of antibiotics from these factory farms ends up in surface water and drives the evolution of MDR microbes. Similarly, the effluent from our hospitals and homes runs into wastewater and produces MDR bacteria.⁴⁹

Given the way factory farming of poultry, pork, and beef is accomplished, it is not surprising that their conditions would breed more virulent and more transmissible viruses. Given that fact, along with the growth of such operations into tropical areas, particularly where bats are endemic, the increase in recombination events that produce novel viral variants is also predictable. In the case of the single-stranded RNA viruses, like Ebola, with their high mutation rate, again it is not surprising that some nonhuman animal variants would acquire the capacity to replicate in humans. We think such an event was responsible for the origin of the SARS-CoV-2 virus.⁵⁰ However, in 2021, there was a growing chorus of responsible scientists suggesting that SARS-CoV-2 might have originated in a laboratory accident.⁵¹ Dangerous viruses have escaped from laboratories before, such as the one that caused the short-lived Ebola outbreak in Russia in 1996.⁵² In the case of SARS-CoV-2, in 2016 a research group from the University of North Carolina, Chapel Hill, in collaboration with researchers at the Wuhan Institute of Virology in China, conducted a gain-of-function experiment. This experiment was designed to test whether a bat coronavirus could evolve the ability to invade human cells. The investigators created a chimeric virus with the bat coronavirus (SHC014) spike protein gene inserted into a mouse-adapted SARS-CoV viral backbone. This virus was then tested against cultured human airway cells, and investigators were able to show that the chimera could use the standard SARS receptor protein (called angiotensin converting enzyme II, or ACE2) and replicate successfully.⁵³ It is also important to know that shortly after the resulting paper was published, the US government ended its support for these sorts of gain-of-function experiments in relation to dangerous viruses.⁵⁴

The obvious question follows: Why would one do this kind of experiment? In my own research we do gain-of-function experiments to better understand microbial evolution to novel environments. Of course, we only use nonpathogenic strains; we have learned from these experiments that evolution still works, and we have learned about the genomic foundations of such evolutionary changes. Given what was already known about the evolution of zoonotic viruses (that is, viruses capable of jumping from other organisms to humans) and their capacity to adapt to new hosts, the results of an experiment to put a bat spike protein gene into the mouse-adapted SARS background should have been obvious. Once again, we learned that evolution works. The difference here is that the experiment was conducted with a potentially dangerous pathogen. Rob Wallace, in his book Dead Epidemiologists, suggests that after gain-of-function experiments were banned in the United States, research may have continued in Wuhan.⁵⁵ The theory that an accidental lab release was responsible is gaining steam, as on May 14, 2021, a letter was published in Science criticizing the World Health Organization’s report on the origin of COVID-19 and suggesting that the laboratory release possibility was viable.⁵⁶

Finally, what about the intentional release of biological weapons? The use of plague organisms in warfare goes back thousands of years. The Romans catapulted the bodies of plague victims or dead cattle into cities. Water supplies were poisoned with the carcasses of dead animals. The British and US governments sanctioned the distribution of smallpox-contaminated and other disease-carrying items to Amerindians in the eighteenth and nineteenth centuries.⁵⁷ In 2013 I wrote a piece for the Encyclopedia of Race and Racism documenting genocide conducted by the Empire of Japan in the Asia-Pacific War.⁵⁸ The piece recounts the operations of Unit 731, which conducted extensive biological warfare against Chinese civilians. The unit was led by microbiologist (and then general) Shirō Ishii, who identified many of the principal attributes required to weaponize biological materials:

1. High morbidity (sickness) and potential lethality

2. High infectiousness or high toxicity

3. Suitability for mass production and storage until delivery without loss of pathogenic potential

4. Suitability for wide-area delivery and sufficient hardiness to withstand the delivery process

5. Relative stability in the environment for extended periods of time after dissemination

6. Potential for use as a biological warfare agent and for improvement by genetic engineering and weaponization processes.⁵⁹

ISHII WAS NEVER HELD RESPONSIBLE FOR HIS WAR CRIMES, IN part because he agreed to work teaching these principles to the United States.⁶⁰

The use of biological agents in warfare is now prohibited by the Biological and Toxin Weapon Convention (BTWC) of 1972. The convention was ratified by 170 nations, but it does not have any inspection protocols, and hiding the potential to devise biological weapons is well within the biotechnology infrastructure of most industrially advanced nations. Indeed, the rapid development of the SARS-CoV-2 vaccines by modern molecular biological protocols indicates that the tools could just as easily be turned to the manufacture of weapons if the need should arise. Worse is the fact that many scientists from nations (or ideological groups) that may have reason to resort to terrorism have been trained in the biomedically advanced nations. Small-scale terrorist and criminal acts using these materials have already occurred.⁶¹

One deterrent to the use of biological weapons is the fact that their high infectiousness often means they cannot be specific in their targeting. However, modern molecular genetic techniques could enable the engineering of biological weapons that target specific genetic markers. Thus, the potential exists for the use of combined markers to target weapons against persons of specific ancestry (e.g., the Chinese could build a weapon that targets persons of European ancestry, or vice versa). Understanding evolution helps us recognize that there is also a hidden flaw to such designs. A viral or bacterial weapon originally targeted toward one group will rapidly evolve the potential to target all. Captain Trips was capable of killing everyone. Applying modern molecular biological tools to warfare is only helping the Doomsday Clock tick ever closer to midnight.

CHAPTER ELEVEN

Homage to Santa Rosalia

or All Hail the Pandemic!