Hi:
I have been sharing some early drafts with people, to give me their feedback and to also provide them some insight into my writing process. Here is another section hot off the press. It is a very rough draft, a section that I decided that I needed just last week, and we will see what the final product looks like. I think that the section will survive, but it may look a bit different than this draft. Right now, that little timeline that is attached is intended to head the section.
Best,
Wade
Speciation, Extinction, and Mass Extinctions
In his Origin of Species, Charles Darwin sketched processes by which species appear and disappear, today called speciation and extinction. Origin of Species is a landmark in science’s history and is still immensely influential. But it was also afflicted by false notions that are still with us. Europe’s emergence from dogma and superstition has been a long, fitful, only partially-successful process. In the 1500s, Spanish mercenaries read a legal document to the unfortunate Indians that they conquered and annihilated that stated that Creation was about five thousand years old, as scholars of the time simply added up the Book of Genesis’s “begats.” The Old Testament is filled with tales of genocide, miracles, and disasters, with a global flood that the faithful Noah survived. As geology gradually became a science, and processes such as erosion and sedimentation were studied, the Judeo-Christian belief of Earth being five thousand years old was discarded and the concept of geologic time arose in Europe.
In the early nineteenth century, there was a dispute personified by Charles Lyell, a British lawyer and geologist, and Charles Cuvier, a French paleontologist. Their respective positions came to be known as uniformitarianism and catastrophism. Just as Britain prevailed in its global imperial competition with France, so did uniformitarianism prevail in scientific circles. Under the comforting uniformitarian worldview, there was no such thing as a global catastrophe, but changes had only been gradual. The British Charles Darwin explicitly made Lyell’s uniformitarianism part of his evolutionary theory, and he proposed that extinction was only a gradual process. While Cuvier did not subscribe to the evolutionary hypotheses that predated Darwin, his catastrophic extinction hypothesis was informed by his fossil studies. But Lyell and Darwin prevailed, and suggesting that there might have been catastrophic mass extinctions in Earth’s past was an invitation to be branded a pseudoscientific crackpot, and that state of affairs largely prevailed in orthodoxy until the 1980s, after the asteroid impact hypothesis was posited for the dinosaurs’ demise. An effort led by a scientist publishing outside of his field of expertise (a Nobel laureate in this instance) removed gradualism from its primacy. It is only since the 1980s that English-speaking scientists could study mass extinctions without facing ridicule from their peers, which has never been an auspicious career situation. Since then, many minor and major mass extinction events have been studied, but the investigations are still in their early stages, partly due to a dogma that prevailed for more than a century and a half, and Lyell’s uniformitarianism is still influential. The ranking of the major mass extinctions is even in dispute, with the Carboniferous period extinction recently argued as greater than the Ordovician–Silurian extinction.
Speciation has probably been more controversial than extinction. To be fair to Darwin, genetics was not yet a science when Origin of Species was published in 1859. It was not until the 1866 publication of an obscure paper by German friar Gregor Mendel that the science of genetics began, but Mendel’s work was dismissed and ignored by mainstream science until the twentieth century. Darwin went to his grave unaware of Mendel’s work. Today, speciation is considered to primarily be a genetic event. But similar to how proteins have several dimensions of structure that dictate their function, and emergent properties that appear at higher levels of complexity, the DNA code by itself does not explain life, although the popular selfish gene hypothesis frames life and evolution as a competition between genes.
Before humans began to alter “natural” evolution with selective breeding, genetic engineering, and the like, speciation has been largely thought to be the result of populations becoming genetically isolated, primarily through geographic isolation, and the isolated populations continue to evolve and adapt to their environments. Eventually, the separated populations become separate species. Even defining what a species is is still controversial, but the general concept is that if two sexually-reproducing organisms can breed and produce fertile offspring, they are of the same species. In light of evolutionary theory, human races are simply genetically-isolated populations that have evolved as they adapted to their environments, but all races can interbreed, so humanity is a single species. Recent DNA studies suggest that white skin is an evolutionary adaptation to northern climates, and white skin may be only six thousand years old. As Europe’s conquest of the world and subsequent Industrial Revolution have ended a great deal of genetic isolation, the adaptive differences seen in the races have been gradually disappearing as multiracial offspring have increased. If humanity attains the free energy epoch, “race” will disappear along with geographic isolation.
Liebig’s Law states that life can only grow as fast as its scarcest nutrient, and nutrient availability is clearly the limiting factor in many ecological situations. In the oceans today, most marine life lives near land (99% of the global fish catch is caught near land), as nutrient runoffs from land feed the oceanic ecosystems. The runoff is seasonal and so is the fish catch, the deposition of marine sediments, and the like. Nitrogen and phosphorous are two particularly critical nutrients, with blooms and die-offs based on those elements’ availability. In the industrial age, with phosphorus and nitrogen artificially added in agriculture, the runoff has created great algal blooms (which create hypoxic “dead zones”) and other events, and even artificially-introduced carbon is a suspected variable.
Since the greatest instances of speciation seem to have happened in the aftermath of mass extinctions, this essay will survey extinction first. A corollary to Liebig’s Law is that if any critical nutrient falls low enough, the nutrient deficiency will not only limit growth, but the organism will be stressed. If the nutrient level falls far enough, the organism will die. A human can generally survive between one and two months without food, ten days without water, and about three minutes without oxygen. For animals, all the food and water in the world are meaningless without oxygen. While some microbes can switch between aerobic respiration or fermentation, depending on the environment (which might be a very old talent ), complex life does not have that ability; all aerobic complex life is oxygen dependent. Also, marine life has adapted to varying levels of oxygen. Birds can go where mammals cannot, flying over the Himalayas, for instance, or being sucked into a jet engine at several kilometers above sea level, due to their superior respiration system. If oxygen levels rise or fall very fast, many organisms will not be able to adapt, and will die.
Biologists consider extinctions to be due to failure to adapt to environmental changes, and the “environment” includes other organisms. But exactly how species go extinct is still poorly understood. There are many interacting variables, including those environmental nutrients, both inorganic and those provided by life forms. The ability of an organism or species to adapt is partly dependent on how specialized it is and how unique its habitat is. Absolute numbers, geographic distribution, position in the food chain (higher in the food chain is riskier), mobility, and reproductive rates all impact extinction risk. During the Cambrian period, about 80% of all animals were immobile. Today, 80% of all animals are mobile. The immobile animals were at higher extinction risk, for obvious reasons.
The evolutionary game for a species is for enough of its members to survive long enough to produce viable offspring. Organisms have adopted myriad survival and reproduction strategies, with astonishing diversity. There are many ways to win or lose that game, but every species eventually loses. More than 99.9% of all species that have ever lived on Earth became extinct. A mammalian species has a life expectancy of around a million years, while a marine invertebrate species has one of about five-to-ten million years. Today’s global extinction rate is more than one hundred times the “normal” rate (“background rate”), and perhaps far greater, due to human domination of the ecosphere.
There are “normal” extinction scenarios, and the “happy ending” extinction is when a species lives, evolves, and there comes a time when it would no longer be able to produce viable offspring by breeding with its ancestors. There obviously would not be a “bright-line” demarcation of such an event, or any way to currently test such an event, but it has likely happened countless times. Another normal extinction begins when a species splits into isolated populations, such as by tectonic plates moving away from each other. Old World and New World monkeys became separated when monkeys from Africa migrated to South America, before the Atlantic Ocean grew to its present size. Isolated populations of a species would continue to evolve and eventually could no longer interbreed, making them different species by definition, and perhaps neither population could breed with its ancestors at the time the populations became separated. Both populations might continue to thrive, but one might find itself in unfavorable conditions and go extinct, while the other continued living. If those isolated populations were still the same species, the population that went extinct would be called locally extinct, but if they were separate species, then the disappearing population would be a species extinction.
Scientists often measure extinction rates at the family and genus levels of the taxonomy, with genera and families being far harder to kill off than species. Some species/genera/families have beaten the odds and survived for hundreds of millions of years. They are called living fossils, and usually all of their close relatives went extinct long ago. The ubiquitous and lowly horsetail is a living fossil, first appearing nearly 400 mya.
Whether more extinctions have been due to “normal” evolutionary processes or catastrophes is debated today. Some kinds of organisms will find great success with their strategies, marginalizing other kinds and even driving them to extinction, to only die off themselves in a mass extinction event, and the previously marginalized life forms will flourish in the post-catastrophic biome. The rise of mammals might have never happened without the dinosaurs’ demise.
The extinction of Ediacaran fauna was the first mass extinction of organisms that could be seen with the naked human eye. There was an extinction of microscopic eukaryotes soon before the eon of complex life began, and there may have been mass extinctions of microbes before then, but the evidence is so thin for anything before then that scientists may never know just how many mass extinctions there were. However, bacteria and archaea, those biochemical wizards, can exist in environments far too harsh for complex life, so there may have been few mass extinctions in Precambrian times.
Mass extinctions always have critical geophysical aspects to them. Continental shelves under shallow seas, which are home to most marine life, are vulnerable to sea level and oceanic current changes. Stagnant waters can lose their oxygen, triggering anoxic events that kill complex life. A continental shelf exposed to the atmosphere by a falling sea level would obviously lose its marine life. Sea levels can rise or fall for different reasons. The most obvious reason has been advancing and retreating ice sheets, but the aggregate continental landmass has always grown (possibly sporadically), and continents can rise and can fall during the journeys of their tectonic plates. Generally, when sea levels fell, the continental shelves lost their marine life, and when they rose, anoxic conditions often accompanied them. There is evidence that the ozone layer has been periodically damaged (1, 2), stressing all plants and animals that the sun shined on. The positions of the continents, both in relation to each other and their proximity to the equator or poles, can have dramatic effects, including impacts on global climate. When global climate changes, new weather patterns can turn rainforests into deserts, and vice versa.
There is also evidence that life itself can contribute to mass extinctions. When the GOE eventually oxygenated the oceans, the organisms that could not survive or thrive around oxygen (called obligate anaerobes) sank into the anoxic margins of the ocean and land. When anoxic conditions appeared, particularly during Canfield Ocean times, the anaerobes could come out to play once again, and when sulfate-reducing bacteria thrived, usually arising from ocean sediments, they produced hydrogen sulfide as a waste product. Since the ocean floor had already become anoxic, the seafloor was already a dead zone, so no harm done there. The hydrogen sulfide became lethal when it rose in the water column, killing off surface life and then wafting into the air and asphyxiating life near shore. But the greatest harm to life may have been inflicted when hydrogen sulfide eventually rose to the ozone layer and damaged it, which could have been the final blow to an already stressed ecosphere. While that may seem a fanciful scenario, there is evidence for it. There is fossil evidence of ultraviolet-light-damaged photosynthesizers during the Permian extinction, as well as photosynthesizing anaerobic bacteria (green and purple), which could have only thrived in sulfide-rich anoxic surface waters. Peter Ward has made this key evidence for his Medean hypothesis, and he has implicated hydrogen sulfide events in most major mass extinctions. An important upshot of Ward’s Medean hypothesis work is that about 1,000 PPM of carbon dioxide in the atmosphere, which might be reached in this century if we keep burning fossil fuels, may artificially induce Canfield Oceans and result in hydrogen sulfide events. Those are not wild speculations, but logical outcomes of current trends and growing understanding of previous catastrophes, proposed by leading scientists. Even if those events are “only” 10% likely to happen in the next century, that we are flirting with them at all should make us shudder, for a few reasons, one of which is the awesome damage that it would inflict on the biosphere, including humanity, and another is that it is entirely preventable with the use of technologies that already exist on the planet.
Mass extinction events can seem quite capricious as to what species live or die. Ammonoids generally outcompeted their ancestral nautiloids for hundreds of millions of years. Ammonoids were lightweight versions of nautiloids, and they often thrived in shallow waters while the nautiloids were banished to deep waters. Both dwindled over time, as they were outcompeted by new kinds of life forms. In the Permian and Triassic mass extinctions, deep-water animals generally suffered more than surface dwellers did, but the nautiloids’ superior respiration system still saw them survive. Also, nautiloids laid relatively few eggs that took about a year to hatch, while ammonites laid more eggs that hatched faster. However, the asteroid-induced Cretaceous mass extinction annihilated nearly all surface life, while the deep-water animals fared better, and the nautiloid embryos that rode out the storm in their eggs were survivors. The Cretaceous extinction wiped out the remaining ammonoids, while the nautiloids are still with us, comprising another group of living fossils. The lystrosaurus is about the only land animal of significance that survived the Permian extinction, and it dominated the early Triassic landmass like no animal ever has, comprising about 95% of all land animals. Why the lystrosaurus, which was a kind of reptilian sheep? Nobody knows for sure, but it looks like it may have been the luck the draw. It seems to be that relatively few bedraggled individuals existed in some survival enclave until the catastrophe was finished, and then they quickly bred unimpeded until the supercontinent was full, for the most spectacular species radiation of all time, at least until humans appeared on the evolutionary scene.
There are many speculated causes for mass extinctions. Before the era of mass extinction investigation that began in the 1980s, a hundred hypotheses were presented in the scientific literature for the dinosaur extinction, but it was kind of a scientific parlor game, with scientists from all manner of specialty concocting their theories. But even during the current era of scientific study of mass extinctions, much is unknown or controversial, with even the data in dispute, much less its interpretation. Dynamics may have conflated to produce catastrophic effects, such as increasing atmospheric carbon dioxide concentration warming the land and oceans to the extent that otherwise stable methane hydrates on the ocean floor and in permafrost would be liberated and escape into the atmosphere. That dynamic is currently suspected to have contributed to the Permian and Paleocene-Eocene extinctions, as well as helping end the Cryogenian ice age. Today, there is genuine fear among climate scientists that those dynamics might return in the near future, as global warming continues and hydrocarbons are burned with abandon, which could contribute to catastrophic runaway conditions. Wise scientists admit that humanity is currently conducting a huge chemistry experiment with Earth, and while the outcomes are far from certain, the risk of catastrophic outcomes is very real and growing.
Recent environmental studies show that disturbed ecosystems can have cascading failures, where the removal of one part of a food chain can collapse the entire chain in cascading failures, where entire ecosystems go extinct. Those cascading events can happen in aquatic and terrestrial environments. Food chains are essentially energy chains made possible by aerobic respiration, and the more complex they are, the more energy is needed to sustain them. I find it striking that the leading hypothesis for why complex civilizations collapse is an energy-scarcity dynamic. Also, the most compelling findings that I have encountered regarding degenerative disease in humans shows that if individual cells no longer have their nutritional needs met by the organism, they stop acting out their role as specialized cells and “go rogue.” It may be difficult-to-impossible for scientists to reconstruct and test cascading failure hypotheses in ancient mass extinction events, but they may have played a major role in them, if not the dominant role.
In summary, mass extinction events may be the result of multiple ecosystem stresses which reach the level where the ecosystem unravels. Other than the meteor impact that destroyed the dinosaurs, the rest of the mass extinctions seem to have multiple contributing causes, with each one ultimately having an energy impact on life processes. The dynamics can be complex, and scientists are only beginning to understand them. This essay will survey mass extinction events and their aftermaths in some detail, as they were critical junctures in the journey of life on Earth.
In 1972, Niles Eldridge and Stephen Jay Gould published their theory of punctuated equilibrium, which has generated plenty of controversy. The basic idea is that species usually evolve slowly and even remain in a kind of stasis, except in certain exceptional times when they evolve relatively quickly. Those exceptional times are often when new ecological niches become available, such as a new biological feature that allows exploitation of previously unavailable niches, or after an ecosystem is wiped clean by a mass extinction. If a creature finds a way of life that works and it can keep exploiting/defending its unique niche, and the niche does not disappear, it can keep doing it for hundreds of millions of years without any significant changes, such as the horsetail, nautilus, and coelacanth have done.
Gene duplication is a major avenue of genetic innovation that leads to speciation, which begins when a gene is duplicated, seemingly in error, and it kind of gets a “free ride,” like a spare part that never gets used. The spare can then “experiment,” which can lead to a new and useful gene, perhaps coding for a new biological feature that enhances an organism’s ability to survive or reproduce. About 15% of humanity‘s genes arose through gene duplication events, and in eukaryotes gene duplication is around 1% per gene per million years. In the wake of mass extinctions, new species appear at high rates in what is called an adaptive radiation. A leading hypothesis is that those post-extinction times allow for a Golden Age where life is easy, without the competition for resources typical in more crowded biomes. In such environments, organisms with duplicate genes and other genetic “defects” survive, and after long enough, those mutations become useful, leading to new species. The most famous such adaptive radiation was the Cambrian Explosion.
Oxygen levels have fluctuated far more than temperature, ocean salinity and pH have during the eon of complex life. Peter Ward has recently hypothesized that fluctuating atmospheric oxygen levels have not only contributed to mass extinction scenarios, but adapting to low oxygen levels has been a key stimulus for biological innovation. In summary, speciation is a reaction of organisms to challenge and opportunity which is eventually reflected in their DNA.
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