Detail: "bk i, pt ii, plt i," illustration for Opticks: or a Treatise of the Reflexions, Refractions, Inflexions and Colours of Light. Also Two Treatises of the Species and Magnitude of Curvilinear Figures. Newton. 1704. Courtesy Boston Public Library.

Read the Reflection, written 4 April 2021, below the following original Transmission.

If there is one thing that the coronavirus pandemic has exposed, it is that there is much that we still don’t know about the world around us. Forget about the trillions — okay, more than trillions — of galaxies in the universe that we’ll never explore. Just at our feet or in the air around us are cohabitants of our own world — viruses — that occupy an odd liminal space, pushing our understanding of the meaning of life. They exist in what is effectively a hidden world, almost a “first Earth” that is both just offstage and right in front of us, and even inside of us. It’s a world teeming with activity, full of blooming, buzzing confusion, competition, and evolution. Sometimes we explore this world intentionally, but at other times we run into it by accident, most noticeably when the alarms on one of the megafauna bio-detectors — people and animals — go off. It’s when these encounters happen that we remember that the space of things we don’t know is truly unfathomable. 

Puttering around on the edge of the known and the unknown is the standard work of science and scientists. While the twinkling of the night sky may often be an inspiration for meditations on how little we understand, it’s actually what we can’t see in the cosmos that is the best reminder of our limited vision. In 1933 Fritz Zwicky observed a huge discrepancy in the amount of gravitational force needed to account for the rotational movement of galaxies and the amount that could be attributed to the visible matter in the galaxy. Naturally, he called this “dark matter.” In 1980 Vera Rubin and Kent Ford used spectrographic data — its own form of making visible the invisible — to show definitively that galaxies contain at least six times as much dark mass as visible mass. As it turns out, Aristotle was wrong: nature loves a vacuum — that’s where it stores most of its gravitational potential.

Countless studies and observations point to the conclusion that nearly 30 percent of the universe is made of dark matter. Dark matter is a big part of what holds the universe together — more stuff for creating attractive forces between things. But, as you may know, ever since the Big Bang, the universe is actually expanding. The cause of this is a different force of darkness, or, rather, something that goes by the name “dark energy.” 

Our understanding of the biological world has also been a story of the discovery of dark matter and dark energy, and our collision with the coronavirus is just the most recent reminder of that theme. Early censuses dramatically underestimated the amount of living matter, a darkness of understanding largely borne of poor optics. Our inability to see at the scale of microorganisms was a source of a good deal of pseudoscience bordering on mythology, especially when it came to disease. “Vapors” and humors were the first dark matter. It was only in the 1880s, twenty years or so after the publication of Darwin’s The Origin of Species, that Robert Koch discovered bacteria and, in so doing, revealed a material cause for infection. Among Koch’s great advances was his use of staining and culturing to make visible the agent of infection. We now know that bacteria and other micro-organisms account for most of the world’s genetic diversity, not only in the environment at large, but also within our own bodies, where our inner microbial ecosystem of the microbiome turns out to be crucial to human health. Some forms of “infection” are deadly, but some are necessary. 

Viruses like the coronavirus are even smaller than bacteria, and so were also dark for some time. They were brought to light in the late nineteenth century, discovered by the Dutch microbiologist Martinus Beijerinck in the course of investigating the etiology of mosaic disease in tobacco plants. Repeated efforts to culture the source of the disease failed, so it wasn’t bacterial in nature — biologists were the first to understand that you need culture to live — but whatever was causing the disease was able to replicate. It was alive in some ways, but dead in others. Beijerinck called this “infectious agent” a virus. 

We now know that a viruses are basically nano-encapsulated genetic information. They have existed from the beginning of biological time, emergent from the proverbial primordial soup, a string of atoms, clumped into molecules, wrapped in another kind of molecular shell, a kind of biological M&M. The raison d’être of the virus is reproduction, which ironically leaves a fair amount of death in its wake. But really, the virus is an engine of life whose dynamics and mechanisms of existence and reproduction make it the agent of genetic expansion, a “dark life” biological force to the dark energy physical force fueling Universal expansion that is dark energy. Not quite twins separated at birth, but siblings separated by several billion years, give or take. 

It is now believed that the nucleated eukaryotic cell, upon which all animal and plant life is based, would not exist were it not for simple viral genes that first copied themselves into ancient host genomes. This led to selection pressures fomenting the formation of cellular membranes and cellular inclusions. It has been hypothesized that without the constant drive from highly mutable viruses there would have been no need for the evolution of recombinational sex — the kind that all animals and plants use, not to be confused with recreational sex!

In a kind of Nietzschean “that which does not kill us makes us stronger” way, any ability that we do have to fight off some diseases can also be at least partly attributed to viruses. Had jawed vertebrates (all vertebrates but lampreys and hagfish) not acquired genes of viral provenance some 500 million years ago, they would have no adaptive immune system and thus minimal means of fending off viruses,

If bacteria had not absconded with viral endonucleases, they would have had no restriction enzymes to protect themselves against viral infection. And without restriction enzymes, our society would have had no science of genetics which made progress based on the unique ability of these enzymes to cleave DNA. Futhermore, CRISPR, the most revolutionary genetic engineering tool in the history of biological science, is effectively the recapitulation of a bacterial anti-virus defense system that kills an infiltrating virus by slicing it into genetic pieces. Current vaccine delivery techniques and other forms of biological therapies rely on a mimicry or instigation of virus insertion mechanisms. What was once dark was eventually brought to light, and once brought to light, helped to bring light — and life. 

Figure 1. VIRAL EDUCATION: This table represents paths from nature to therapy. It shows viral genetics (viral innovation) that have been co-opted by other forms of life (exapted adaptation) and that have been used as a part of human genetic engineering (engineering utility).

Our all-too-human tendency to focus on what is directly or instrumentally visible, or of comparable scale to ourselves, has blinded us to both the largest and smallest scales of the universe — scales where physical forces shape the elementary structure of matter. We are also blinded to those living scales invisible to the eye that have shaped the form and function of adaptive matter. The COVID-19 crisis has made the terrifying dark energy of evolution visible and has brought us closer than is comfortable to the engines of selection. We live in an invisible ocean of microbial diversity and menace, one that is insensitive to the transience of multicellular life. Maybe now is the moment for us as a culture to learn from our microbial allies in the universe of dark matter — the bacteria — from whom we acquire our symbiotic microbiome — that the best way to defeat the dark energy of the virus is to turn its entropic ingenuity against itself and out-evolve the virus by evolving our scientific ingenuity, and probably our social practices too. We’ll have to adapt; what choice do we have? 

David Krakauer
Santa Fe Institute

Dan Rockmore
Dartmouth College
Santa Fe Institute

T-030 (Krakauer & Rockmore) PDF

Read more posts in the Transmission series, dedicated to sharing SFI insights on the coronavirus pandemic.

Listen to SFI President David Krakauer discuss this Transmission on episode 34 of our Complexity Podcast.


April 4, 2021


In our article, “Out-Evolving COVID-19,” we wanted to stress the fact that much of the matter selected and formed through evolutionary processes is effectively invisible to us—a biological manifestation of a much more general process in the sciences, where the space of “unknown unknowns” is, well, unknown, but present. We generally knock up against it by accident, sometimes manifest to our senses (even if requiring a technological assist), at other times a nagging error term in a model (mathematical or otherwise) that had looked like it was working, only to come up short in some new and unanticipated environment or dataset. That’s the scientific process: you’re right until you are wrong.

Dark matter and dark energy were inferred through a deeper and more careful understanding of the universe, identified as important parts of the engine that drives evolution on the scale of galaxies. Microbial dark matter works closer to home and has exerted a powerful influence on the evolution of life. We tabulated how many of the adaptations that we consider constitutive of being a mammal had their origin in our ancient entanglements with viral environments.

Looking back over the last year, the evolutionary force of infection speaks for itself. The virus attacked vulnerable human populations based on comorbidities precipitously terminating social life. As it transitioned from the dark to the light—and was attacked by vaccine makers—the original virus evolved and evolved again as variants spilled forth in an ongoing co-evolution with the vaccine-making process. This kind of evolutionary force—even as extended to the world of health sciences—was expected.

What was unexpected—at least to us, and thus outside of our discussion—was the way it would spill over from the sphere of natural history into that of cultural history. Not only were humans host to SARS-CoV-2, but in a larger sense, communities, companies, transport networks, treasuries, and nations all played host to the pathogen. This terrible pandemic was a natural experiment reminding us that not only were we blissfully ignorant of phenomena at the scale of the microbe, but also that there were dark elements driving an evolution of the fundamental structures of society.

Mutational events and selective pressures worked through the biology of genetic elements, endonucleases, and introns. Their “epi-viral” effects were now felt in travel and supply networks, the elastic markets of Main Street, the inelastic resilience of Wall Street’s forecasting mechanics, and, most of all, in a fear of death that quickly transformed the basic social dynamics of modern interpersonal relationships. Spheres of friendship shrank quickly to encompass only close family. The fundamental materials of the social fabric frayed and eroded. The “triumph” of globalism—at least in the West—had elided the basic dark energy of tribalism, which needed only a push from a lethal pandemic to come (back) to light. In essence, the virus had not just leapt species, but it had leapt scales—it was zoonotic on the scale of societies.

Ever since Darwin puzzled over the social life of bees, with their altruism and sterile casts, and the gaudy displays of birds that render them conspicuous and vulnerable to predators, biologists have pondered the question of the levels of selection. What does selection see: the gene, the cell, the whole organism, or the population? And, by extension, what does a virus infect: a cell, an organism, or a community?

Richard Dawkins argued that, ultimately, it is only the gene that matters and persists, and that everything larger, from bodies to populations and species, are just forms of bookkeeping that allow us to track nature’s true currency. Genes are our coinage and bodies merely organic bank accounts or blockchains that record nature’s transactions.

Over the last several decades we have gained a deeper understanding into this question, largely through the use of mathematical models, and now understand better that selection can work at any level that respects a few key constraints. These include the relative rates of replication versus dispersal, and the rates of contact with one’s own descendants. And the results of these models are to show that evolution operates at a multiplicity of scales. The same sort of argument might be made for a virus infecting a community or a company. As long as that community or company is densely connected, and as long as the virus depends on their internal organization to be spread—from office layouts, org charts, and water-cooler sites—then we can justifiably speak of social or corporate hosts.

And why does this matter? It matters for much the same reason that understanding immune systems is important for the control of microbial infection within the body. We are really talking about the mechanisms of robustness: How, after 2020, we should rethink the robustness of society from the ground up. And how we might use our understanding of the working of the innate and adaptive immune system within the organism to modify social life, work spaces, travel, and economic support, to minimize the effects of infection at these higher levels of organization.

So, what have we learned? We now understand that the host of a virus extends beyond the cell and body to the social networks, communities, and cities in which “life” takes place. We thought that treating a disease meant finding cures, palliatives, and vaccines on the level of the organism—that all we needed were the tools of biological sciences. What we failed to grasp was its effect at scale and the remediations required of the downstream social, economic, and even political behaviors. We can no longer see a virus as just a minimal form of life that expands by siphoning the energy of bodies. It is one of the forms of dark matter shaping all complex systems at every scale of existence.

Read more thoughts on the COVID-19 pandemic from complex-systems researchers in The Complex Alternative, published by SFI Press.