Wednesday, August 19, 2015

The Sixth Extinction: Reading Notes

I just finished Elizabeth Kolbert's Sixth Extinction, about the the five mass extinctions of living things known from the fossil record, and the one that appears to be underway right now, courtesy of human activity.  I bought the book almost by accident (wanted Amazon free shipping on unrelated items); it came highly recommended, but I expected it to be very depressing to read.  Instead, it is so artfully written that I wish the subject were one for more optimism.

This is not a review of the book, but rather a sort of summary--as much for me as anyone, so I don't lose track of the most important details.

Kolbert organizes the book into thirteen chapters each of which focuses on a species that is, or likely soon will be, extinct.  Some, but not all, can be laid to our doorstep.  The order of the chapters is not chronological, but arranged to tell a series of overlapping stories, beginning with a recent extraordinary extinction that spurred Kolbert's interest, passing into the history of the idea of extinction, then the discovery and research into mass extinctions and their causes, and then other recent and future extinctions that tell something of the dangers we have created for myriad species.  Within each chapter the organization is loose, and woven around Kolbert's own travels to explore current research around the world.  She gets up close to people and species, but is never in the way.    She views her topic with clear-eyed compassion but without undue optimism.  She ends her prologue: "If extinction is a morbid topic, mass extinction is, well, massively so.  It's also a fascinating one.  In the pages that follow, I try to convey both sides: the excitement of what's being learned as well as the horror of it.  My hope is that readers of this book will come away with an appreciation of the truly extraordinary moment in which we live."

Chapter One: The Sixth Extinction

Panamanian Golden Frog (Atelopus zeteki) recently driven into extinction with breath-taking speed by rapidly-spreading human-imported chytrid fungus (really alga) (Batrachochytrium dendrobatidis) that is still wiping out amphibians to this day.  Kolbert visits the El Valle Amphibian Conservation Center, and goes frog-hunting with the Panamanian director valiantly trying to save endangered frogs on a shoe-string budget by keeping captive populations free from the fungus.  Kolbert briefly explores the concepts of mass extinction and background extinction rates.

Chapter Two: The Mastodon's Molars

American Mastodon (Mammut americanum) died out at the end of the last ice age, though most likely at the hands of the first Americans.  Bones discovered in Ohio went to famed French anatomist George Cuvier, who was the first to prove conclusively (President Thomas Jefferson's hopes notwithstanding) that living species had, in fact, become extinct.  Legions of amateur "fossilists" brought to light more and more bones of animals that no longer lived on Earth.  Inspired further by new geologic maps of the Paris basin, he declared that extinction was not a slow event, but brought about by sudden "revolutions on the surface of the earth."  Cuvier's catastrophism put him at odds with Charles Lyell's uniformitarianism, and his intimate knowledge of "correlation of parts" of each living thing led him to reject Darwin's natural selection.  He deserves to be remembered for much more than these.

Chapter Three: The Original Penguin

The Great Auk (Pinguinus impennis) was driven extinct largely by sailors who provisioned their ships with the easily-captured bird of North Atlantic shores.  The last birds were killed only a few years after Charles Darwin journeyed around the world aboard HMS Beagle as captain's companion and ship's naturalist, and Charles Lyell wrote his three-volume Principles of Geology that so influenced young Darwin.  Kolbert visits Iceland, whose offshore islands hosted the last few auks, and explores the uniformitarianism of Lyell, and wonders at Darwin's seeming disinterest in species extinction.

Chapter Four: The Luck of the Ammonites

The ammonite Discoscaphites jerseyensis died along with all ammonites, dinosaurs, and others in the end-Cretaceous mass extinction.  Kolbert tells in depth the moving story of the Alvarezes and their discovery of the impact that most probably caused it, the resistance by the paleontological establishment due partly to tribalism, and partly to an inherited dislike of catastrophism.  She discusses the change in the "rules of the survival game" that come with a mass extinction: that, in effect, "time and chance happeneth to all things," so that being well-adapted is no hedge against extinction in the mass extinction crap-shoot.

Chapter Five: Welcome to the Anthropocene

The graptolite Dicranograptus ziczac went extinct with many others in the first of the known mass extinctions at the end of the Ordivician, an extinction probably linked to glaciation.  Kolbert explores the discovery of the big five mass extinctions, and the paradigm shift of "what is sometimes regarded as neocatastrophism, but is mostly nowadays just regarded as standard geology, [which] holds that conditions on earth change only very slowly, except when they don't."  She discusses the "Nemesis hypothesis," noting a brief tendency to attribute every mass extinction to an impact.  She delves a little into the current theories of the causes behind other mass extinctions.  She discusses the newly-named Anthropocene, and the mass extinction now underway in it.

Chapter Six: The Sea Around Us

The limpet Patella caerulea, like most calcifiers, is endangered by ocean acidification resulting from increasing levels of atmospheric CO2.  Kolbert dives near Ischia in the Mediterranean, where CO2 seeps provide a natural laboratory for exploring ecosystem changes caused by acidification.  She explores the nuances of the issues faced by calcifiers--any organisms from coccolithophores to mollusks to echinoderms--that draw carbonate from seawater to form part of their structure.  The speed at which humans are putting carbon dioxide into the oceans probably exceeds even that during the Permian extinction. 

Chapter Seven: Dropping Acid

Acropora millepora is one coral in the Great Barrier Reef endangered by warming ocean water as well as ocean acidification. Besides the usual issue with calcification, the warmer temperatures cause the symbiotic zooxanthellae algae the polyps depend on for food to produce dangerous concentrations of oxygen free radicals, and the coral polyps respond by evicting them.  Coral reefs are the oases in sterile tropical seas, creating the basis for highly diverse and productive ecosystems.  As one researcher told her, "if you don't have a building, where are the tenants going to go?"  Reefs have a long history on earth, but they have been built by various animals from rudist bivalves of the Cambrian to stromatoporoids of the Silurian to rugose and tabulate corals of the Devonian.  Since the Permian extinction, more familiar corals have taken over.  Periodically coral reefs disappear during mass extinctions, finally being built again after millions of years.  In addition to the big dangers, corals face the usual suspects: over-fishing, agricultural runoff, deforestation, and dynamite fishing. 

Chapter Eight: The Forest and the Trees

Alzatea verticillata, a tree that is the only species in its family, is among the thousands of tree species Kolbert encounters journeying among Miles Silman's seventeen two-and-a-half acre study plots that dot a mountain ridge in the Peruvian Andes.  Because of their highly-limited altitudinal ranges, each plot--lying at a different altitude--could have an almost entirely different flora.  Silman laid out these plots in 2003, and already had interesting results after only a few years.  Study of the tree census data from these plots shows that the forest is already in motion, as tree species migrate toward higher elevations in the face of climate change.  Since species vary in their response, ecosystem structure will change, and some existing symbioses be broken.  Kolbert explores the species-area relationship, "which has been called the nearest thing the discipline has to a periodic table."  The much-publicized 2004 study seeking to get an estimate of extinctions caused by climate change used the SAR in combination with current ranges of a thousand-odd plant and animal species, and a range of assumptions on how mobile these species were.  Although much criticized, further work has found its conclusion (that somewhere between about ten and thirty percent of species could be gone by 2050) is not unreasonable. 

Chapter Nine: Islands on Dry Land

Eciton burchellii is an army ant that can be found in some of the Amazonian "island" reserves of Brazil's Biological Dynamics of Forest Fragments Project (BDFFP)--one of the largest and longest-running experiments.  Amazonian landowners seeking to develop their properties were persuaded to allow researchers to preserve "islands" of forest in satisfying the legal requirement that fifty percent of a property remain undeveloped.  (Other areas of undeveloped forest serve as controls.)  Kolbert discusses the idea of replacing biomes with "anthromes" totalling 39 million square miles versus unpeopled "wild lands" totalling 11 million square miles.  In light of the fragmentary nature of much of even this minority of Earth's surface, the forest fragmentation studies are even more important.  Further developing the species-area relationship, Kolbert notes that, for example, BDFFP reserves don't show the assumed diversity drop to a new equilibrium, but instead have dropped in diversity steadily with no end in sight.  As populations become smaller, they become increasingly vulnerable to bad luck: drought, storms, disease, and the like.   BDFFP reserves that are big enough to support a few army ant colonies don't support the obligate ant-birds found elsewhere: the army ants become dormant for periods of time, and when by chance the few ant colonies in a reserve become dormant simultaneously, the ant birds are eliminated.  American naturalists Carl and Marian Rettenmeyer, spending more than half a century studying Eciton burchellii, listed more than 300 species that live in association with them.  

Kolbert further discusses estimates of current extinction rates and their flaws.  Terry Erwin's pesticide fog-fueled estimates of as many as 30 million species of arthropods on the planet has been trimmed to a still-impressive two million to seven million insects--possibly because he overestimated the number of species-specific insects (one-fifth, by his results).  E.O. Wilson's famous calculation of a extinction rate 10,000 times the background has not been borne out by observation: it may be that slow "relaxation" has led to an "extinction debt," or that habitat destroyed might regrow, or simply that the many unknown species of e.g. insects mean that we are missing many of the extinctions.  Or any combination of these. 

Chapter Ten: The New Pangaea

The Little Brown Bat (Myotis lucifugus), among many other American bat species, is doomed by the White-nose Fungus, Geomyces destructans, that comes from Europe.  It was first discovered in a cave not far from Kolbert's own town.  So begins her treatment of the problem of alien invasive species; our mixing of species willy-nilly likened to rejoining all the continents into a single land mass.  (Which would not be as destructive as what we've done: in a true Pangaea many barriers to migration would still remain.)  Even ignoring the many species of non-indigenous pets that yearly cross borders (more that the number of natives in toto), vast numbers are moved accidentally.  Applying the species-area relationship to a virtual new Pangaea shows that we stand to keep only a third of Earth's mammals and fifty percent of its birds--from that single cause alone.

Chapter Eleven: The Rhino Gets an Ultrasound

Attempts to conserve the Sumatran Rhino (Dicerorhinus sumatrensis) were a tragedy of errors.  (For example, four of the seven sent to US zoos died before keepers realized they needed fresh leaves and branches, and couldn't survive on hay.)   There are now probably fewer than a hundred animals left in the wild.  Of the four other species of rhino, only one is not threatened or endangered.  The rhino is one of many examples of animals that are "two big to quail"--safe from most predators from an early age.  But large animals have suffered disproportionate extinction in the Anthropocene--we have changed the rules of the game.  Kolbert discusses the arguments--going back to Lyell, Darwin, Wallace--for climate change vs. our ancestors as the chief cause.  The preponderance of evidence now implicates humanity.  Jared Diamond commented, "Personally, I can't fathom why Australia's giants should have survived innumerable droughts in their tens of millions of years of Australian history, and then have chosen to drop dead almost simultaneously precisely and just coincidentally when the first humans arrived."  A study of spores left in sediments from fungi that live in large animal dung shows that, prior to any climate change, humans doomed Australia's giants simply by increasing their mortality enough to tip them into decline; and their end led to build-up of fuel and fires that then changed the vegetation to fire-tolerant species.

Chapter Twelve: The Madness Gene

Homo neanderthalensis was our closest remaining relative until its disappearance thirty thousand years ago.  Kolbert discusses our imagined relative--from bent-over brute to flower child to something a little more evidence-based (and even one given a shave and a suit).  Svante Paabo's sequencing of neanderthal DNA and his discovery that most humans have a modest amount of neanderthal DNA (and later discovers the Denisovans) leads Kolbert to compare modern human and ape capabilities, concluding that, for all their intelligence, chimps don't collaborate the way we do.  Paabo points out that, although Neanderthals spread widely, they never crossed water big enough that they would have been out of sight of land.  But "we never stop," he says.  And, "we are crazy in some way.  What drives it?"  

Visiting a cave famous for its paintings, Kolbert says, "It is often speculated that the humans who sketched on the walls of the Grotte des Combaralles thought their images had magical powers, and in a way they were right.  The Neanderthals lived in Europe for more than a hundred thousand years and during that period had no more impact on their surroundings than any other large vertebrate.  There is every reason to believe that if humans had not arrived on the scene, the Neanderthals would be there still, along with the wild horses and the wooly rhinos.  With the capacity to represent the world in signs and symbols comes the capacity to change it, which, as it happens, is also the capacity to destroy it.  A tiny set of genetic variations divides us from the Neanderthals, but that has made all the difference."

Chapter Thirteen: The Thing with Feathers

Homo sapiens is endangered by itself: Richard Leakey warned that, "Homo sapiens might not only be the agent of hte sixth extinction, but one of its victims."  By disrupting the biological and geological systems on which we depend, we're putting our own survival in danger.  Kolbert visits the Frozen Zoo belonging to the San Diego Zoo, which stores cell cultures of nearly a thousand species, some of which are no longer extant.  (With time that proportion will grow.)  then she visits next door with a lone Hawaiian crow and the dedicated keeper who is trying to get sperm from him to increase the captive population.  Although she applauds the dedicated efforts to preserve individual species, they do not change the overall pattern of extinction.  She muses over the root cause of the Sixth Extinction: "To argue that the current extinction event could be averted if people just cared more and were willing to make more sacrifices is not wrong, exactly; still, it misses the point.  It doesn't much matter whether people care or don't care.  What matters is that people change the world."

She ends, "the Sixth Extinction will continue to determine the course of life long after everything people have written and painted and built has been ground into dust..."


  1. This comment has been removed by the author.

  2. This is an excellent book and one recommended for my grad program. After reading it, what do you think should be done to slow or reverse the effects of extinction rates?

  3. This is an excellent book and one recommended for my grad program. After reading it, what do you think should be done to slow or reverse the effects of extinction rates?

  4. So what do you think we must do to change the world?

  5. Huge question. At risk of shooting from the hip, here. Causes of extinction include climate change/ocean acidification, habitat destruction and fragmentation, invasives, pollution and overharvesting. Some obvious moves are reduced greenhouse gas emissions (combined with geoengineering the climate because this ship will take many decades to turn), protecting endangered habitat the way the US now protects endangered species, common-sense laws and regulations against movements of species in ships, cargo, etc., applying US-style pollution standards world-wide, and serious woldwide restrictions on fishing. All requiring unprecedented levels of international cooperation. Behind all of this, though, is an enormous and still growing human population with desire for very resource- and energy-intensive lifestyles. That population needs to come down to a tiny fraction of what it is now, and in the meantime the first world needs to cut way back and the rest of the world temper its expectations. All of this MIGHT cut back on the destruction, and maybe save us as well.