The Sixth Extinction – Elisabeth Kolbert – 2014

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The same way acoustical engineers speak of “background noise” biologists talk about “background extinction”. In ordinary times extinction takes place very rarely, more rarely even than speciation, and it happens at what’s known as the background extinction rate. For mammals, the best-studied group, it’s been reckoned to be roughly 0.25 per million species-years.  Since there are 5500 mammal species, at the background rate you would expect one species to disappear every 700 years.

The history of life thus consists of “long periods of boredom interrupted occasionally by panic”. Conditions change so dramatically or so suddenly that evolutionary history counts for little.

Toward the end of the Beagle’s voyage, Darwin encountered coral reef. Darwin saw that the key to understanding coral reef was the interplay between biology and geology. If a reef formed around an island or along a continental margin that was slowly sinking, the coral, by growing slowly upward could maintain their position relative to the water. If, eventually, the land sank away entirely, the reef would form an atoll.

The evidence became pretty strong for the impact at the end of the Cretaceous, 65 million years ago. In the process of excavating the enormous crater, the asteroid blasted into the air more than fifty times its own mass in pulverized rock. As the ejecta fell back through the atmosphere, the particles incandesced, lightning the sky and generating enough heat to broil the surface of the planet. Owing to the composition of the Yucatan peninsula, the dust thrown up was rich in sulfur. Sulfate aerosols are particularly effective at blocking sunlight. After the initial heat pulse, the world experienced a multiseason “impact winter”.

The Ordovician (Godwana, all lands form one giant mass) followed directly after the Cambrian, which is known, for the explosion of life. The seas was filled with creatures we would more or less recognize (starfish, sea urchins, snails, nautilus, trilobites, sea scorpions, reef and clams. On land there were mosses and Liverworts. At the end of Ordovician, some 444 million years ago, oceans emptied out. Something like 85% of marine species died off. This is seen today as the first of the Big Five extinctions.

The current theory is that the end-Ordovician extinction was caused by glaciation. For most of the period a so called greenhouse climate prevailed – carbon dioxide levels in the air were high and so, too, were sea levels and temperatures. Right around the time of the first pulse of extinction, CO2 levels dropped. Temperature fell and Gondwana froze. Sea levels plummeted and many marine habitats were eliminated. The ocean’s chemistry changes, with cold water holding more oxygen. One theory has it that glaciation was produced by the early mosses that colonized the land and, in so doing, helped draw carbon dioxide out of the air. If this is the case, the first extinction of animals was caused by plants.

The End-Permian extinction also seems to have been triggered by a change in climate. But in this case, the change went in the opposite direction. 252 million year ago there was a massive release of CO2 into the air, so massive that geologist have a hard time even imagining where all the carbon could have come from. Temperatures soared, the seas warmed by as much as 10 degrees and the chemistry of the ocean went haywire. The water became acidified, and the amount of dissolved oxygen dropped so low that many organisms probably suffocated. Reef collapsed. This lasted some 100 to 200,000 years. By the time it was over some 90% of all species had been eliminated. Even intense global warning and ocean acidification seem inadequate to explain losses on such staggering scale. On hypothesis is that heating of the oceans favored bacteria that produce hydrogen sulfide which is poisonous to other form of life.

A recent study of pollen and animal remains on Easter Island concluded it wasn’t humans who deforested the landscape; rather it was the rats that came along for the ride and then bred unchecked. The native palms could not produce seeds fast enough to keep up with their appetite.

Since the start of the industrial revolution, humans have burned through enough fossil fuel to add some 365 billion metric tons of carbon to the atmosphere. Deforestation contributed to another 180 billion tons. Each year we thrown up another 9 billion tons or so, an amount that ‘s been increasing by 6% annually. Every day, every American in effect pumps three kilograms of carbon into the sea. Thanks to this the pH of the ocean’s surface waters has already dropped from 8.2 to 8.1.The pH scale is logarithmic, so even such a small numerical difference represents a very large real work change. The decline by 0.1 means the water are 30% more acidic than they were in 1800.

Castello Aragonese provide a perfect preview of what lies ahead for the oceans, owing to the CO2 pouring out of the vents nearby. All told, one-third of the species found in the vent free zone were no-shows in the pH 7.8 zone. Unfortunately, the biggest tipping point, the one at which the ecosystem starts to crash, is mean pH7.8. which is what we expect to happen by 2100.

Ocean acidification will alter the availability of key nutrients, like iron and nitrogen. It will change the amount of light that passes through the water and will alter the way sound propagates (and make the sea noisier). It seems likely to promote growth of toxic algae. It will impact on photosynthesis – many plant are apt to benefit from elevated CO2 levels – will alter the compound of dissolved metals, in way that can even be poisonous. Acidification will affect significantly the group of creatures known as calcifiers (sea urchins, starfish, clams, oysters, crustaceans, corals. Calcifiers must join calcium ions and carbonate ions to form calcium carbonate. At the site of calcification, organisms must alter the chemistry of the water to, in effect, impose a chemistry of their own. Acidification increases the cost of calcification by reducing the number of carbonate ions available.  If the water is too corrosive, solid calcium carbonate begins to dissolve. This is why limpets that wander too close to the vents at castello aragonese end up with holes in their shells.

The great reef extends, discontinuously, for more than 2,600 km, and in some places it is a hundred and fifty metres thick. Sea cucumbers are animals whose closest relation are sea urchins.

The biosphere 2 in the late 1980’s was largely funded a billionaire Edward Bass. The project was widely considered a failure, the biospherians, 4 man and 4 women for 2 years, spent most of their time hungry  and they lost control of their artificial atmosphere. Decomposition, which taxes up oxygen and gives off carbon dioxide, was supposed to be balanced by photosynthesis, which does the reverse. For reason having to do mainly with the richness of the soil that had been imported into the “agricultural zone”, decomposition won out.

Saturation state with respect to calcium carbonate” (or aragonite with is the calcium carbonate corals manufacture) is important as acidification: it’s a measure of the concentration of calcium and carbone ions floating around. When CO2 dissolve in water it forms carbonic acid H2CO3 which eats carbonate ions, lowering the saturation state. Corals grew fastest at an aragonite level of five, slower at four, and still slower at three. At the level of 2 they basically quit building (below one the water is unsaturated, and calcium carbonate dissolve). As saturation levels fall, the energy required for calcification will increase, and calcification rates will decline. As reef are constantly eaten away at by fish and sea urchins and worms, and also battered by waves and storms, reef must always be growing just to stay even.

A recent study found that the Great Barrier Reef coral cover has reduced by 50% in the last 30 years. Another paper concluded that in the next 50 year or so all coral reef will cease to grow and start dissolve.

Reef gap occurred after the late Devonian and late Triassic extinctions, and it took millions of years for reef construction to resume.

Each individual polyp is an animal and a host for a microscopic plant know as zooxanthellae. The zooxanthellae produce carbohydrate, via photosynthesis, and the polyps harvests these carbohydrate. Once water temperature rise past a certain point, zooxanthellae produce  dangerous level of concentration of oxygen radicals. The polyps react by expelling them. As Zooxanthellae is also the source of the colors the corals appear to turn white (coral bleaching).

The latitudinal diversity gradient: as a general rule, the variety of life is most impoverished at the poles and richest at low latitudes. Diversity in boreal forest is low: across Canada’s billion of acres of it, you will find only about 20 species of tree. In Peru, a small plot can contain up to 1055 tree species…

On theory holds that organisms can produce more generation in the tropics. The greater the generation, the higher the chance for genetic mutations and the greater the likelihood a new species will emerge. Also a possible theory is that higher temperature lead to higher mutation rates. Another theory posits that what is important in the tropics is that temperature are relatively stable. Species possess a relatively narrow thermal tolerances and small climatic differences (hills, valleys) constitute barriers. Populations are more easily isolated, and speciation ensues. Another theory centers on history: the tropics are old (many millions of years for the Amazon forests) and there has been a lot of time for diversity to accumulate.

It is now believed that ice ages are initiated by small changes in the earth’s orbit, caused by, among other things, the gravitational tug of Jupiter and Saturn. These changes alter the distribution of sunlight across different lattitudes at different times of the year.

The “species area relationship” (SAR)  has been called the closest thing ecology has to a periodic table : the larger the area you sample, the greater the number of species you will encounter. The correlation is not linear. Rather it is a curve that slopes in a predictable way (logarithmic as with increasing surface areas, the number of new species increase by a lower ratio). S= cAz  where S is the number of species, A the surface area, c and z are constants that vary according to the region and the taxonomic group.

One model has it that as temperature climbed, creatures colonized any new area that met the climate conditions they were adapted to. Still many species ended up with nowhere to go. As earth warmed, the conditions they were adapted to simply disappeared (the disappearing climates turned out to be essentially in the tropics). Other species saw their habitat shrink because to track the climate they had to move upslope, and the area at the top of the mountain is smaller than at the base.

Taking mid-range scenarios for warming projection, the group concluded that 24% of all species would be headed toward extinction.

There is no reason to suppose that a warmer world would be less diverse than a colder one. One the contrary, it is possible that a warmer world would be more varied. In the short term, though, things look very different.

In the ups and downs of the Pleistocene, we are at the crest of an up. Temperature for the last 2.5 million years never got warmer than they are now. There has been no advantage in being able to deal with extra heat.

To find carbone dioxine level higher than today requires going back 15 million years. It is possible that by the end of this century, CO2 levels reach a level not seen since the Antartic palms of the Eocene, 50 million years ago.

The question is; have plants and animal retained over the huge amount of time – whole radiations of mammals have come and gone in this period – the potential characteristics that would allow them to change their metabolism and manufacture special protein to adapt? What if they have lost these costly characteristics because for some many millions of years they provided no advantages?

Currently 130 million square kilometers of land are ice free. People have directly transformed more than half of this land, mostly by converting it to crop land and pastures, building cities, mining quarrying etc. Of the remaining 60 million square kilometer, 3/5 are covered by forests ‘natural but not necessarily virgin’.

What happen when you cut down the surrounding forests: gradually both the number and variety of birds in the remaining fragment of forest started to drop and kept on dropping. There was not suddenly a new equilibrium with fewer species. And what went for birds went for other groups as well. Diversity drop off with isolation. The process is know as ‘relaxation’ (gradually reducing number of species): smaller areas harbor smaller populations and smaller population are more vulnerable to chance. When local extinction occur (more often in small areas) there may not be any species to recolonize the land.

Amazon is a megadiverse ecosystems where every single species is very, very specialized. In these system there is a huge premium on doing exactly what you do. A natural corollary of high diversity is low population density, and that is a recipe for speciation. Diversity is self-reinforcing. But it adds to vulnerability, since small isolated populations are much more susceptible to extinction.

Calculation made 25 years ago assume that 1% loss of territories lead to 0.25% loss in the number of species. With a very conservative estimate of 2 million species in the tropics, this means 5,000 species lost each year, 14 a day or 1 every 100 minutes.  10,000 times the natural rate of extinction. This is not what we see today. There is seem to be a lag to the process, a gap. This is referred to as “extinction debt”. It is possible that habitat loss to deforestation is not really lost: forests can regrow. It is possible that the reason why observation don’t match prediction is that we are not very observant. Extinctions will affect insects and invertebrates mostly so we do not notice this and we don’t even know to the nearest million how many species there is in the tropics.

Recent study show that changes in land use in the Amazon also affect atmospheric circulation. This means on a large enough scale, destruction of the rain forest could result not just in a disappearance of the forest but disappearance of the rain.

The process of remixing the world’s flora and fauna, which began slowly along the routes of the early migration, has, in recent decades, accelerated to the point that in some part of the world, non native plants now outnumber native ones. During any 24 hours, it is estimated that 10,000 species are being moved around the world just in ballast water. Thus a single supertanker can undo millions of year of geographic isolation.

Why some introduced species are able to proliferate explosively is matter of debate. A new transported species has left behind its rivals and predators. The corollary to leaving old antagonists behind is finding new, naïve organism to take advantage of (and those have no protection against the new comer).

Before European arrived, New England has no earthworms: the region worms had all been wiped out by the last glaciation and, even after 10,000 years of relative warmth, north American worms had yet to recolonize the area.

APASD the Asian Pacific Alien Specie Database.

Visitors to Antarctica in a single season brought some 70,000 seeds from other continents. Already one plant species, a grass from Europe, has established itself in Antarctica. Since Antarctica has only 2 native vascular plant species, this means that a third of its vascular plant are now invaders. In Hawaii, a new invader is added each month (compared to one every 10,000 years before human settled Hawaii). The immediate effect is a rise in local diversity. But because of this, global diversity has dropped.

Megaherbivores generate mega amounts of shit. This provide sustenance for a fungi known as sporormiella. Sporormiella spores are tiny but durable and can be identified in sediments that have been buried for tens of thousands of years. Study shows that 50,000 years ago, sporormiella counts were high. Then, rather abruptly around 41,000 years ago, sporormiella counts dropped almost to zero. Following the crash, the landscape started to burn (tiny grains of charcoal) and the vegetation in the region shifted to more dry adapted plants, like acacia. If climate drove the megafauna to extinction, a shift in vegetation should precede a drop in Sporormiella. But just the opposite has happened. The only explanation that fit the data was “overkill”.

Study in north America shows that even a very small initial population of humans – a 100 or so – could, over the course of a millennia or 2, multiply sufficiently to account for pretty much all the extinctions in the record. All they had to do was to pick off a mammoth or a giant sloth every so often and keep this up for several centuries. This would have been enough to drive the population of slow reproducing species first into decline and then all the way down to zero.

Chimps do a lot of smart things. But the main difference is that chimps don’t have collaborative project: they don’t put their head together, you would never see two chimps carry something heavy.

Injuries on Neanderthals bones may reflect the rigors of hunting with the neanderthals’ limited repertoire of weapons. The Neanderthals never seem to have developed projectiles.

Modern human must have interbreed with Denisovans, too, because contemporary New Guineans carry up to 6% Denosovan DNA.