Why don’t we measure biodiversity?

By John Upton

Vast resources are plowed into measuring the metrics associated with global warming. Calculations reveal that American and European greenhouse gas emissions are falling while China’s are rising, and that more carbon dioxide is being pumped out worldwide every year than had been the case the year before. We know that carbon dioxide levels passed a record-breaking 400 parts-per-million point in May, well above the preindustrial level of 280 ppm, before dipping in line with normal seasonal fluctuations — that knowledge is courtesy of air monitoring in Hawaii and the findings of ice-core studies. And gravity-measuring satellites are used to estimate the rate at which glaciers are melting — revealing that despite harboring just 1 percent of the world’s land ice, these thawing rivers of ice are responsible for 29 percent of the rise of sea levels.

The results of these measurements don’t just keep us awake at night. They help policy-makers target efforts to reduce emissions and to prepare communities for changes in the climate.

But what about biodiversity?

Although the world is rallying around efforts to come to terms with its climate problem (even if not enough is being done to actually solve that problem), it is failing to measure the alarming decline of biodiversity, which by one recent estimate has fallen 30 percent in 40 years. It is not investing the resources needed to track the genetic stockpile contained in the cells of plants, animals, mushrooms and other forms of life as forests are bulldozed, rivers are diverted and acidifying oceans are overfished.

Every time a species or a jungle is lost, and every time environmental tumult helps generalists (such as ring-billed gulls) outcompete specialists (such as piping plovers), the world loses some of its genetic code. That code is critically important. It can help an ecosystem weather changes in the, well, in the weather, which is happening now more than ever in human history. It can help sustain a myriad of complex food chains that underpin the very functioning of the natural world. And it can present humans with chemical compounds that prove useful as new drugs or foods.

If we are to get a handle on the specifics of the biodiversity crisis, which we must do if we are to effectively manage the problem, then more scientists need to be trained and employed and provided with the resources needed to advance their fields.

Aware of the problem of falling biodiversity, the United Nations last year formed the Intergovernmental Platform on Biodiversity and Ecosystem Service. The group is structured a bit like the Intergovernmental Panel on Climate Changeits primary function is to review, assess, synthesize and share information about biodiversity with policy makers.

Illustrated by Perry Shirley.
Illustrated by Perry Shirley.

The group held meetings in Malaysia this week to discuss two main topics: the measurement and assessment of genetic and biological resources; and the calculation of the value of key ecosystem services.

The conclusion: The world just isn’t doing enough to measure biodiversity.

“Of the estimated 10.8 million species on land and in the oceans, less than 2 million have been scientifically described,” IPBES chairman Zakri Abdul Hamid, science advisor to Malaysia’s prime minister, said in a statement published Wednesday at the end of the three days of talks. “If we don’t know what species there are out there, we don’t know what niche they fill in a healthy ecosystem or perhaps in remedying some human condition.” More from the statement:

Most world nations – unanimously committed to protecting biodiversity – nevertheless cannot measure and assess their genetic and biological resources, nor the value of key ecosystem services nature provides to them, international experts from 72 countries warned today.

In addition to taxonomists, nations lack economists able to put a value on the water purification, storm protection and other services of nature, which would inform trade-off choices in development planning. And fewer still deploy social scientists to estimate nature’s non-economic (e.g. cultural) values, or to find ways to effect needed changes in human attitudes and behaviour.

“There’s an old saying: We measure what we treasure. Unfortunately, though we profess to treasure biodiversity, most nations have yet to devote adequate resources to properly measure and assess it along with the value of ecosystem services,” Zakri said. “Correcting that is a priority assignment from the world community to IPBES.”

Human infections are dead ends for valley fever fungus

By John Upton

People infected with two closely-related species of fungi are dying in growing numbers in the American southwest. The Coccidioides spores are blown with dust into lungs, where they can trigger a painful and sometimes-deadly condition known as valley fever.

But any cocci that ends up in a human has hit a dead end. It will not reproduce to spawn a new generation.

That’s because of the lifecycle adopted by these varieties of cocci after evolving with the rodents that share their desert home. The coccis’ ancient ancestors lived and dined on plants. Then they evolved to feast instead on the rotting flesh of dead animals. Now they have evolved to live inside a living mammal, sometimes waiting for years for the host to die so they can pounce and quickly consume the fresh kill.

Illustrated by Perry Shirley.
Illustrated by Perry Shirley.

Mammals whose immune systems can’t control the fungus may die quickly. But as I explain in Vice’s Motherboard blog, most animals that are infected with cocci develop few symptoms — and those symptoms are normally short-lived:

Normally, [the Cocci] eek out lives as filaments called hyphae. The hyphae live in the soil and produce spores, a lucky few of which get sniffed into the lungs of desert rodents. The spores balloon in size inside the host, forming spherules. The mammal immune system kicks quickly into gear at this point, building walls around the spherules, containing them and developing immunity against further attacks.

It’s when the immune system fails to contain these spherules that the fungus can propagate throughout its victim, sometimes with deadly consequences. As an infected rodent dies, collapsing into the desert, the cocci burst out of suspended animation and unleash streamers of hyphae that eat the rotting meat. As the fungus feasts, hyphae and spores slip back into the soil, ready to start the cycle all over again.

Humans don’t slip into the desert sands when we die. We are embalmed or cremated, making any infection a waste of time for the fungus and, in some cases, a waste of life for humanity. “If a cocci spore gets into a human, it has made a big mistake,” John Taylor, a University of California at Berkeley mycologist, told me. “It’s unlikely to ever become adapted to living in humans.”

Black-backed woodpeckers would face extinction without wildfires

By John Upton

Illustrated by Perry Shirley.
Illustrated by Perry Shirley.

This summer has been a tinder-dry scorcher in the American West, where climate change is being blamed for a horror fire season. Mountain snow is melting earlier nowadays and summers are getting hotter — and that perilous partnership is fueling a steady surge in the frequency and size of the region’s wildfires.

The infernos kill firefighters, destroy homes and damage public infrastructure.

But it’s worth remembering that fires are healthy and regenerative phenomena in many ecosystems — including those in the West.

Blazes clear out water-hogging undergrowth and provide blank slates upon which timberlands can grow anew, boosting forest biodiversity. Rugged pods that encase the seeds of some specialized plants open after fire, sowing the genesis of the next generation in fertile fields wiped clean of competitors.

It’s not just plants that have evolved to rely on fire. Woodpeckers, for example, can flourish in its wake. The black-backed woodpecker has a particularly specialized diet that leaves it dependent upon the charred aftermath of wildfires. The species feasts on the wood-boring beetles that proliferate in burned trees following blazes in Western American mountain-ranges.

Rim Fire
The aftermath of the Rim Fire, the fourth-largest wildfire in Californian history, photographed near Yosemite National Park in early September by San Francisco journalist Chris Roberts.

But us humans are not as fond of fire as are the beetles or the woodpeckers that hunt them. Public policy dictates that fires should be avoided and, if that fails, confronted without compromise. The practice of preemptively thinning out forests to reduce fire impacts, and the logging of forests after they burn, have both taken heavy tolls on the black-backed woodpeckers.

Populations of these birds have been harmed so severely by public policies of wildfire suppression that the federal government is reviewing whether genetically distinct populations in two regions should be added to its list of endangered species.

“This is the first time in the history of the Endangered Species Act that the government has initiated steps to protect a wildlife species that depends upon stands of fire-killed trees,” Chad Hanson, an ecologist with Earth Island Institute, said when the U.S. Fish & Wildlife Service announced the review in June.

A clean-up following the Rim Fire, making it more difficult for black-backed woodpeckers to inhabit this area. Photo by Mike McMillan of the U.S. Forest Service.
A clean-up following the Rim Fire, making it more difficult for black-backed woodpeckers to inhabit this area. Photo by Mike McMillan of the U.S. Forest Service.

Hanson coauthored research published in May in The Open Forest Science Journal that showed just how severely one of those two populations of woodpeckers, which lives in the Sierra Nevada and southern Cascade ranges of California and Oregon, has been affected by humanity’s wont to battle fire. Hanson and his colleague, Dennis Odion, obtained data from the government and from their own observations which they used to model the effects of typical wildfire suppression policies in the Sierra on the species’ habitat.

“A scenario based on thinning 20 percent of mature forests over a 20-year period, and post-fire logging in 33 percent of potential habitat created by fire, reduced the amount of primary habitat after 27 years to 30 percent of the amount that would occur without these treatments,” the scientists wrote in the paper.

“Our results indicate that conserving the distinct population of black-backed woodpeckers in the southern Cascades and Sierra Nevada and the biodiversity for which they are an indicator will require that more unthinned area be burned by wildfires and protected after fire as critical habitat.”

The following table was lifted from the paper. It compares the amount of black-backed woodpecker habitat available within a study area following 27 years of simulated fire suppression policies:

woodpeckers and fire

And this photograph of an acorn placed in the trunk of a Rim Fire-charred pine is an endearing reminder that wildlife perseveres following fire. Wild Equity Institute founder Brent Plater tells me it might have been put there by a squirrel or a scrub jay — but that it was most likely the handiwork of an acorn woodpecker. “Caching acorns in tree cavities is what they do for a living,” he said.

Photo by Chris Roberts
Photo by Chris Roberts

Flight Behavior, by Barbara Kingsolver

flight-behaviourClimate change affects the entire globe, but its effects are felt locally. It nudges animals from one area to another, it changes local weather patterns, and it takes a toll on the men and women who till and cultivate the soil so that the rest of us may eat.

Barbara Kingsolver understands all of this. Flight Behavior, published last year, is a touching tale of an unusually warm and wet Appalachian winter and its effects on a hardscrabble farm. The unseasonable season is made all the more extraordinary by the arrival of a wayward rabble of migratory butterflies.

An ambitious protagonist trapped with young kids and a dull husband in a small town is thrust suddenly into a harsh spotlight shone by the insects that she discovered. And while struggling with newfound fame, the young mother comes to grips with the changes ravaging the tiny world around her.

Kingsolver is one of modern literature’s greatest practitioners. It’s a delight to see her take on climate change with this thought-provoking yarn. The story is imbued with a scientifically-refined grasp of global warming and loaded with well-placed cynicism of the media’s coverage of this most pressing issue.

John Upton

These chicks puke at predators

By John Upton

When Eurasian rollers forage for insect prey for their young, they’re not just on a quest for nourishing fat and protein. They’re fossicking through an ecological armory for chemical weapons.

Some plants produce toxins to deter herbivores. Some insects that eat those plants use those plant toxins for their own defense. Eurasian roller chicks use the plant toxins from those insects to produce a pungent orange liquid — an unsavory concoction that scientists have concluded is used as a defense against predators.

A team of Spanish researchers found that Eurasian roller nestlings vomited when they picked them up, but not when they approached the young birds, talked to them or gently prodded them. “This fact suggests that the vomit might be produced in response to some kind of predators that actively grasp and move prey during the predation event such as snakes, rats and mustelids, which are common predators of hole-nesting species as rollers,” the scientists wrote in a paper published in the journal PLOS ONE.

Illustrated by Perry Shirley.
Illustrated by Perry Shirley.

The researchers collected the puke and smeared some of it on pieces of chicken, which they offered (with the smeared side hidden) to 25 dogs alongside a similar chunk of poultry smeared only with water. Some of the mutts strangely showed no appetite for chicken whatsoever. But 18 of the 20 dogs with a hankering for hen opted first for the untreated meat, indicating that the smell is off-putting for a predator. Most of those 18 dogs subsequently wolfed down the vomit-smeared chicken, but six of them left it entirely alone.

“One could wonder about the nestling advantage of this defence,” the scientists wrote. “Kin selection is a possible answer to that question because a predator that finds the first nestling of a brood of five to be distasteful may leave alive the others.”

From where do the chicks get the hydroxybenzoic and hydroxycinnamic acids, phenolic acids and psoralen needed to produce their unpalatable puke?

The scientists matched these compounds to toxins produced by plants to deter animals from feeding on them. Many insects have developed an immunity to such toxins, and some use the plants’ toxins to defend themselves. That’s the case for many of the grasshoppers upon which the rollers prey, and the scientists believe that the chicks are, in turn, purloining the poisons from the grasshoppers to defend themselves.

But that’s not all — the scientists think that the parent birds might also be hunting for more-poisonous insects, such as centipedes, that most other birds would never touch.

“Grasshoppers are the main prey that rollers hunt to feed their nestlings,” they wrote. “Furthermore, rollers feed their offspring with a large share of poisonous arthropods that are avoided by most of the other sympatric insectivorous birds. This suggests that rollers are resistant to these toxic substances and could have the ability to sequester chemicals from their protected prey to defend themselves.”

An adult Eurasian roller.
An adult Eurasian roller in Kazakhstan. Photo by Ken and Nyetta.

Research: Bat-killing fungus arrived from afar

By John Upton

A ripple of bat deaths has grown since 2006 to become millions of Chiroptera deep, stretching out from its New York epicenter into five Canadian provinces and west at least as far as Missouri. The latest state to be affected was Minnesota, where infected bats were discovered in two parks.

The dead bats were all members of species that hibernate — and they succumbed to white nose syndrome. The disease is caused by a fungus that eats away at their wings and faces.

Little brown bats are among the worst affected. These adorably tiny bats were common throughout Eastern America as little as a decade ago, sucking down mosquitoes and other pests during their nocturnal maunders. Now the species appears to be on the verge of being listed as federally endangered.

Illustrated by Perry Shirley.
Illustrated by Perry Shirley.

Mammals appear to have developed high body temperatures to help stave off infections of fungi. But hibernating bats have a chink in that armor: When they hibernate, their body temperatures plummet. And when most bats hibernate, they huddle together, which helps the fungal infection spread through the slumbering colony.

What caused this fast-moving fungus to suddenly begin attacking bats? Did it go rogue, evolving from a soil eater into a devourer of bat flesh? Or is it an invasive species that arrived from some far-flung place?

A pair of Wisconsin-based U.S. Forest Service scientists studied the DNA of the disease along with that of more than a dozen species of other fungi found growing in bat caves in the eastern U.S. What they found, first and foremost, was that the pathogen was not quite what everybody thought it was.

Scientists have called the disease Geomycetes destructans since it was identified in 2009. But the recent research, described in the journal Fungal Biology, indicates that the fungus is actually a member of the genus Pseudogymnoascus. Hence, it has been reclassified P. destructans.

Of the other species of Pseudogymnoascus fungi sampled in the studied hibernacula, the scientists reported that none were closely related to P. destructans. That’s significant, because it suggests that white-nose syndrome arrived in New York from some other part of the world, perhaps on the shoes of a traveler or shipped in as a few spores with freight.

Researcher Andrew Minnis said the study is part of a wider effort to find a way to protect bats from the fungus. “Once key elements of this [fungus] species’ biology, including mechanisms of pathogenicity, are identified, it will be possible to target them,” he said.

Once it was realized that many related fungi were present in bat caves, but weren’t killing bats, “thoughts arose that these species could be used for comparative purposes — to understand why P. destructans is different,” he said. Following the findings from this study, “further and more informed comparative work can now be performed.”

Confirmed and suspected white-nose syndrome cases. Map updated August, 2013 by the U.S. government.
Confirmed and suspected white-nose syndrome cases. Map updated August, 2013 by the U.S. government.

Recommended novel: Lexicon, by Max Barry

Click to buy from AmazonA cultish group of self-described poets has mastered the art of persuasion – by figuring out which words and sounds can be used to hack the brains of different personality types. When the poets’ lab develops a word so powerful that almost nobody can resist being coerced by it, at least one among them uses it to destroy an Australian mining town.

This is a high-octane action novel with a hefty mix of science fiction and a touch of old-fashioned romance.

Being a dual Australian-American citizen, I enjoyed this novel in part because its literary set spanned Washington, D.C. and the Australian outback. And I absolutely loved Max Barry’s dry Australian sense of humor, which left me laughing out loud at the most surprising moments.

— John Upton

Recommended novel: Fallen Land, by Patrick Flanery

Click to buy.This deftly subdued thriller charts the dovetailing lives of five members of three tormented families living in a corner of a subdivided farm.

An old widow squats in the farmhouse where she was born, grieving as her ancestral land is carved up, torn up and developed around her. The new neighborhood is left partly built when the developer goes bust, losing his wife, kids, home and sanity along the way.

When a family moves in next door to the widow — into the model home where the developer intended to house his own family, replete with a secret bunker and passageways — only the youngest among the new tenants knows a terrifying secret: In this house, they are not alone.

This is a remarkable story — not just for its riveting plot and creative storytelling, but for the deep connections that Patrick Flanery explores between Americans and the places they call home.

This might never be marketed as an environmental novel, but the story drips with a cynical exposé of the desecration of urban planning by failures of modern democracy.

— John Upton

Recommended novel: The Appeal, by John Grisham

Click to buy.John Grisham paints a bleak picture of how justice can be bought and sold in America.

After a chemical factory sickens the residents of a small town, a team of local attorneys secures a colossal — and precedent-setting — payout for one of its many victims. But before an appeal can reach the Mississippi Supreme Court, the factory’s owner sets about replacing a centrist judge on the state bench with one that is controlled by industry.

This gloomy tale of environmental injustice reveals the shortcomings of the very concept of judicial elections.

— John Upton

Recommended novel: Breath of Death, by Saad Shafqat

Click to buy from Amazon.On one level, this is a well-composed thriller that thrusts medical researchers into a race against a bio-terrorist. On another, it’s an exploration of the challenges that scientists face in Pakistan – and the discrimination they can face when they attempt to collaborate with their peers in America.

An exciting story by a talented Pakistani author who grasps the cultural and financial divides that hold science in the East asunder from that in the West.

John Upton

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