Friday, April 13, 2018

The Sixth Extinction: An Unnatural History

Book Review: The Sixth Extinction: An Unnatural History (Henry Holt & Company, 2014)

This was a fair to good book, mainly a history of mass extinctions and of extinction in general. Kolbert is a writer at The New Yorker and has written about environmental and science topics. I moved this up on my review list since the author just gave a talk about the book at the local university.

She begins with the recent evolutionary success of humans who have managed to vastly increase their population in the past 100 years and vastly affect their environments and planet to the point where we are directly influencing an unprecedented acceleration of the rate of extinction of many species, mainly through habitat loss. Humans began causing extinctions thousands of years ago by hunting animals to extinction, including isolated island species, especially flightless birds, and very likely megafauna as well. When we discovered and developed fossil fuels and subsequent technologies we expanded our population which also expanded human-caused extinctions.

The first chapter is about the Panamanian golden frogs, once extremely populous, now disappearing. She travels to the area to observe efforts to keep the frogs from going extinct. Frog and amphibian extinctions in general have been accelerated recently, even though some have been present on Earth for hundreds of millions of years and several made it through all of the previous mass extinctions. A fungus in the chytrid family, known as Bd for short, is the culprit killing the Panamanian golden frogs.

She talks about what is known as the ‘background extinction rate’ which is the normal rate of extinction for a class of organisms. For example, the current background extinction rate for mammals is 0.25 per million species-years, or roughly one lost mammalian species every 700 years. In contrast, mass extinctions cause substantial biodiversity losses rapidly and globally. They happen close enough in time to be called events, although an event may last hundreds of thousands of years. Mass extinctions often mark the boundaries of geologic periods. The Big Five mass extinctions were: 1) End of Ordovician, 2) End of Devonian, 3) End of Permian, 4) Late Triassic, and 5) End of Cretaceous. According to paleontologist David Raup: the history of life consists of “long periods of boredom interrupted occasionally by panic.” There have been many lesser extinction events as well. Amphibian background extinction rates have not been calculated due to a dearth of amphibian fossils, but it is thought to be less than that for mammals. However, in recent times, most herpetologists have seen several extinctions of amphibian species. In fact, now they are considered the world’s most endangered class of animals, possibly as much as 45,000 times the background extinction rate! Many reef-building corals, fresh-water mollusks, sharks and rays, and mammals are also endangered.

The Bd fungus was thought to have been introduced by importing frogs from other places that were less affected by it. Introduction of invasive species and new diseases is another result of human travel. Humans have managed to globally re-shuffle species, both purposely and accidentally, on an unprecedented scale.

Oddly, humans did not understand that species went extinct until fossils were interpreted by paleontologists. There were theories and ideas about fossils, often referred to the flood of Noah in Genesis. In the late 1700’s the French naturalist Nicolas-Frederic Cuvier interpreted Mastodon fossils from America as remnants from an extinct species. The author visits a paleontology museum in Paris that houses Cuvier’s specimens and sketches. It was Cuvier who established extinction as fact, she notes. He found many fossils in nearby gypsum quarries. The discovery and reconstruction of the bones of the Ohio mastodon by others would cement Cuvier’s idea of extinction. In 1812 Cuvier published a four-volume compendium on animal fossils. Cuvier was also involved in early study and identification of dinosaur fossils. Cuvier’s success (perhaps modest by modern standards) was based on his keen knowledge of anatomy. His senior colleague Jean-Baptiste Lamarck, who asserted that there was a force pushing beings toward complexity (an idea that later merged into Darwin’s evolution) opposed his idea of extinction.

Cuvier believed extinctions were caused by catastrophic events that happened very quickly. Not much later this idea would become known as ‘catastrophism’ and it was the basis of early geological theory in the early-mid 1800’s until Charles Lyell appeared on the scene. Lyell observed rock layers and concluded that geologic processes like sedimentation and erosion were very gradual over long periods of time. He also thought extinction was a gradual process. Darwin read his books as a young college student at 22 as he traveled on his famous voyage to Galapagos Islands and beyond to the South Pacific. He experienced a horrific earthquake while in Chile and measured the local ground uplift with surveying instruments to eight feet. These and other experiences convinced him of the truth of Lyell’s ideas as Lyell also talked about uplift and subsidence, noting that over long periods of time accumulated uplifts could make mountains. Darwin noticed that coral reefs and atolls were a result of the interplay between biology and geology in that sea shelves subsided (dropped) and reefs moved accordingly to waters of shallow depths. He presented the idea to Lyell who was delighted and revised his idea of reefs which erroneously thought underwater volcanoes were the underlying source. Lyell was wrong about other things – ie. catastrophes and destructive events do have a place in geology. Darwin’s key idea of natural selection was also rooted in Lyell’s ‘gradualism’ and followed Lyell’s famous principle that “the present is the key to the past.”

She visits a museum in Iceland that houses the last known specimen of the great auk, an extinct bird, large and flightless, last known from the mid-1800’s. Once numbering in the millions, the bird is one of many species of animals wiped out by humans for food. Darwin also acknowledged human-caused extinction, which in some cases could be directly observed as hunted species became more and more rare.

Next, she considers the ammonites and the work of the Alvarez’s (Luis and his son Walter) in determining their demise was caused by an asteroid impact that defines the end-Cretaceous mass extinction, the stratigraphic boundary being known as the K-T boundary. Paleontologists went around the world looking for the K-T boundary contact in outcrops and successive rock layers before and after, Geochemists got involved looking for evidence of asteroid impact minerals, mainly irridium. Finally, the impact crater was actually found at the Yucatan Peninsula of Mexico. It was not the impact itself that caused the ammonite extinction, wrote the Alvarez’s, but likely the dust which blocked out the sun which killed plants and animals. This is the event that wiped out the dinosaurs. Living things near the impact were simply vaporized. The atmosphere was altered and the ocean chemistry. Species that could live in deeper ocean water had better survival rates. Ammonites can be seen very well in the fossil record to decrease in variety and in amount but in this case the seemingly gradual was really precipitated by a single event. The end-Cretaceous (K-T) mass extinction is thus far the only one (probably “the” only one) confirmed to be from an impact event.

Next, she considers a history of the science of extinction in terms of Thomas Kuhn’s “paradigm shifts” in his historical/psychological study of scientific revolutions. The first paradigm shift was acknowledging extinction which happened with Cuvier and contemporaries in the 1800’s. Lyell’s focus on the gradual was another shift. That idea held up until evidence for asteroid impacts showed that mass extinctions could result from a single catastrophic event. Of course, in reality both gradual and catastrophic processes operate in geology with the catastrophic simply being much rarer than the gradual.  

She goes to Scotland where geologists are looking at graptolite fossils at the end-Ordovician (444 million years ago) boundary defined by the first major mass extinction. Life then was in the sea, having “exploded” in variation in the previous age, the Cambrian. They are looking for the record in the rocks where the sea went from habitable to inhabitable. After verification of the impact explanation for triggering the end-Cretaceous mass extinction, impact was a popular idea for other mass extinctions. However, lack of iridium and other factors favor other explanations. The current theory in favor for the end-Ordovician mass extinction is that of global cooling and glaciation of a previous greenhouse climate. The glaciation dropped global sea levels drastically which ruined sea life habitat and ocean chemistry changed drastically as well. This dropped previously high CO2 levels which cooled the planet further. One idea has it that it was the spread of mosses on the land that decreased CO2 levels and triggered the process. She considers this idea, that it was plants that caused the first major mass extinction. The end-Permian extinction also appears to be a result of changes in climate.  A massive increase in atmospheric CO2 happened then, 252 million years ago. The seas warmed. Reefs collapsed. Some scientists think the CO2 came from volcanos. Some also think that the conditions eventually favored bacteria that produced hydrogen sulfide and that this extended the die-off due to a poisoned atmosphere.

She explores the notion that we have entered a new geologic age informed by humans and the effects of their population growth and technology. Dutch chemist Paul Crutzen termed it the Anthropocene. He noted that humans have transformed between a third and a half of the land surface of the earth, dammed and diverted most of the rivers, added excess nitrogen to the biosphere through fertilization, overfished the oceans, and use half of the world’s freshwater runoff. We have also altered the chemical composition of the atmosphere and the ocean.

Next, she goes to an area in the Tyrrhenian Sea off the coast of Italy where there is an active underwater volcano system that spews CO2 from vents on the ocean floor. Scientists there can study the effects of increased ocean CO2 as one moves closer or further from the source. The extra CO2 produced by humans is partially absorbed by the ocean and this lowers its pH making it more acidic. Scientists there study the effects of more acidic ocean on sea life, particularly life that makes calcium carbonate shells. Some creatures are more adaptable than others, but few can live in the very low PH waters very near the vents. The same is true of a globally acidified ocean – some species will thrive and others suffer. The general prediction is of loss of biodiversity. Ocean acidification was involved in the end-Permian and end-Triassic extinctions and possibly the end-Cretaceous as well as the Toarcian Turnover 183 million years ago in the early Jurassic. Shelled organisms that use calcium carbonate, ie. calcifiers, need to adjust their internal chemistry to the ocean chemistry. Typically, they do that through evolution so the speed at which they can evolve will be a factor. There are no calcifiers near the vents.

Continuing with the effects of ocean acidification on calcifiers she travels to the Great Barrier Reef region in the South Pacific. Corals are a calcifying superorganism. Darwin was right that subsidence is a major factor in reef building. She travels to One Tree island to observe the work of atmospheric scientist Ken Caldeira and others. Caldeira thinks that the coming ocean acidification will surpass that of the last 300 million years. Thus, coral reefs could be the most vulnerable of ecosystems. They are already being affected. She explains pH and calcium carbonate saturation. The sea provides a buffering effect on acidification but the amount of CO2 is increasing the amount of carbonic acid to exceed the buffering effect. In the geologic record limestone-based reefs have come and gone but those reefs consisted of different organisms, many now extinct. Modern coral reefs face other threats too: overfishing that increases algae which compete with the corals for nutrients, agricultural runoff which also spurs algae growth, and siltation resulting from deforestation. Increasing water temperatures cause the corals to lose their colorization mechanisms. This is known as “coral bleaching” and can lead to the death of reefs.

Next, she heads to the Andes in Peru where researchers are studying the effects of climate on the region’s immense biodiversity through observing plots of trees confined to very specific elevations based mainly on temperature. These species are very specific in their requirements. Some species can move upslope faster than others by projecting seeds but others can succumb more easily to rising temperatures. The worry here is that many of the less versatile species will go extinct. The logic is that since there is much greater species variation in the tropics there will much more climate change related extinction there. The trees also host other species of insects, etc. that also have rather exacting condition requirements. One theory simply holds that the tropics have more species precisely because those species are more condition-specific. Another theory notes that it is the age of the tropics in terms of less disruption over time than in temperate and polar zones. They have had more time to diversify. New species are still being discovered in the tropical regions. Species do migrate but if the rate of climate change, mainly increasing temperatures but also differing water conditions, exceeds the rate of migration, some species won’t make it. She explains the species-area relationship graph (S=cAz (z is a superscript – power). What humans change mainly is A or area, changing the availability of certain types of land through development and agriculture. One prediction is that by 2050 9-13% of species will be committed to extinction under the minimum warming scenario and 21-32% by the maximum warming scenario. Others disagree, saying species are better at adaptation and moving. Most do not think that climate change and habitat destruction will cause a major extinction like the big five but may approach some of the minor ones. (Thus, the book’s title may be deceptive. Even the book’s subtitle is questionable since extinction is quite natural as 99.5% of species once in existence have gone extinct. A person asked this question at her talk and she conceded that it may not have been the best subtitle). The tropics have other threats: illegal logging, illegal ranching, and illegal mining. Some have noted that in a warmer world, species’ overall biodiversity will eventually increase rather than decrease as evidenced in the warm Eocene of 50 million years ago. The problem now is that warming is happening much faster than species can keep up.

Next, she moves s over to the Amazon in Brazil to observe some of the “reserves” kept from development – patches or fragments of rainforest. There she visits famed conservationist Tom Lovejoy who convinced the Brazilian government to preserve parts of the area for scientific study. The experiment started in the 1980’s. Here also, new species continue to be discovered. The preserved plots are essentially islands among logged out areas. Like the Andes experiment these areas are megadiverse and species are very specific in actions and in conditions required for thriving. High species diversity also means low population density and so species become isolated by distance. Such populations are much more susceptible to extinction. She notes that while primary forest is declining in the Amazon the amount of secondary forest is growing so this may slow the high species extinction rate predicted somewhat. Timbered forests will regrow if not further developed. There are so many species in the tropics it is hard to count them, let alone count how many have gone extinct.

Next, she considers what has been called the “New Pangaea,” the globalization of species by virtue of human introduction, both deliberate and accidental. Thus, the geographic distribution of some species has advanced hugely. Here she focuses on the loss of bats in Eastern North America due to a fungus that causes what is called “white-nosed syndrome.” This was first observed in 2007 and is killing bats by the millions, especially when they hibernate in caves and mine shafts in the winter. Ballast water of ships, hitching rides on people and cargo in planes, and on people’s stuff and shoes from car travel are some of the ways species expand their distribution. Invasive species have become problematic in many places although some are more problematic than others and some may also be beneficial, ie. introduced species are not always invasive species but often are. Here she explores some of the stories of introduced species. They often become invasive because in new areas their usual predators may not be around. Introduced species can actually hunt other species to extinction as happened with the brown tree snake accidentally introduced from Papua New Guinea to Guam where it extinctified some birds and bats. It merely did what humans do – succeeded at the expense of other species. As in the story of the American chestnut tree succumbing to a fungus that was common to Asian chestnut trees that the fungus evolved with, the fungus killing American bats is not harmful to bats in Europe from where it was likely introduced. The same is true of the chytrid fungus killing the Panamanian frogs. Novelty can kill. She goes through a surprising list of species introduced to North America: dandelions, honeybees, earthworms, queen-Anne’s lace, burdock, plantain, etc. Currently, the emerald ash borer is a problem here in Ohio – I have about 40 or 50 of these trees dying or dead within about 500 ft of my house. Some will fall a limb at a time or maybe from the base. Others nearer will have to be cut down in the next few years. Zebra mussels and Asian carp are aquatic species that have wreaked havoc. Of course, humans have been introducing species from time immemorial as they travelled to new areas. It is just in recent times the process has been vastly accelerated. This has resulted in rises of ‘local diversity.’ While local diversity has been increasing, global diversity has been decreasing.

Next, she visits the Cincinnati zoo which houses (not sure if still there) a Sumatran rhinoceros named Suci. They are the oldest and smallest of the five species of rhinos today but highly endangered. Some housed at zoos are trying to be mated to reproduce. These are known as ‘captive breeding’ programs. The Sumatran rhino, once common from Bhutan to Indonesia, is a victim of habitat destruction and forest fragmentation. There are only a few hundred left in the wild. In their case captive breeding efforts have made the problem worse as many died faster in captivity. A few have been born in captivity so there is some hope. Other rhinos have been overhunted for their horns which are used as an aphrodisiac in Chinese medicine and apparently as a party drug where they are powdered and snorted like cocaine.

While in Cincinnati she also visits the nearby museum at Big Bone Lick where the old mastodon fossils that Cuvier interpreted were found. She considers whether the North American megafauna were driven to extinction by human hunters (the leading theory by far) or by climatic changes or possibly by both. Similar losses of fauna occurred in Australia, New Zealand, Madagascar, and other places. Of course, every loss coincided with the arrival and persistence of humans in those areas. She shows through scientific evidence that pre-historic humans almost certainly caused these extinctions. One issue with some of the big megafauna is that they reproduce sparingly and have one baby at a time so that even a small amount of them killed by humans could have a large effect on their population in a relatively short period of time. Other simulations have shown that the megafauna were very vulnerable to humans, that only a few hundred humans could have wiped them out over a millennium.

Next, she visits Germany to consider the fate of our human deep ancestors, the Neanderthal. The likelihood is that modern humans, homo sapiens, simply killed off and inter-breeded with Neanderthals. Genetic projects are underway to map the Neandertal genome, compare it to the genome of modern humans, and find out where and possibly when they diverged. Apparently, it is a slow process since getting DNA from Neanderthal bones is not easy. We now know that Europeans and Asians share more Neanderthal DNA than Africans. All non-Africans carry between 1% and 4% Neanderthal DNA. Only modern humans, not Neanderthals, used projectiles and made it to Australia, Madagascar and other places (used boats). Paabo, the researcher there in Germany, is a leading DNA-extracting researcher in the realm of humans. He tried and failed to extract DNA from a bone fragment from 17,000 year old homo floresiensis, first discovered in 2004 in Indonesia and identified as a new species. Then in 2010 the first bones of the Denisovans were discovered in a cave in Siberia. Paabo named the species and was able to extract DNA from the finger bone discovered. It was found that modern people from Papua New Guinea share 6% DNA with Denisovans but that modern Siberians and Asians do not. This is likely due to ancient migration patterns. The Neanderthals used tools, buried their dead, and some think they made art and adorned themselves, but after living in Europe for 100, 000 years there is little to show of their “culture.”

Finally, she explores the San Diego zoo, specifically the place there where the DNA of extinct species is preserved. Here there are also very endangered species. One is a rare male alala, or Hawaiian crow named Kinohi. These crows can imitate human speech somewhat like parrots. They are trying to extract his sperm to mate with the few female alalas left. She talked about him in her talk.

Overall, this was a pretty good book and a nice overview of extinction in general. Like I said before, I don’t think the title or the subtitle are ideal since this may not become a “mass” extinction although the rate of extinction has certainly accelerated significantly – and it is not at all unnatural. I think she talked a bit much in her talk about the effects of climate change and the current American political climate as being unhelpful. I would have rather explored more about biology in general.

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