Take a Deep Breath and Say Hi to Your Exposome

Pig-Pen in his element (Illustration: Charles M. Schulz)

by Richard Conniff/Scientific American

Over the past few decades, researchers have opened up the extraordinary world of microbes living on and within the human body, linking their influence to everything from rheumatoid arthritis to healthy brain function. Yet we know comparatively little about the rich broth of microbes and chemicals in the air around us, even though we inhale them with every breath.

That struck Stanford University genomics researcher Michael Snyder as a major knowledge gap, as he pursued long-term research using biological markers to understand and predict the development of disease in human test subjects. “The one thing that was missing was their exposure” to microbes and chemicals in the air, Snyder says. “Human health is clearly dependent not just on the genome or the microbiome, but on the environment. And sampling the environment was the big hole.”

In a new study published September 20 in Cell, Snyder and his co-authors aim to fix that, with a wearable device that monitors an individual’s daily

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“The Dinosaur Artist” Review: Bad Boy Makes Old Bones Big Business

by Richard Conniff/The Wall Street Journal

On a Thursday afternoon in May 2012, a paleontologist named Bolortsetseg Minjin was having lunch near the American Museum of Natural History in New York when she heard a news broadcast about a spectacular dinosaur being put up for auction. It was a specimen of Tarbosaurus bataar, a 70-million-year-old close kin and look-alike of Tyrannosaurus rex.

Heritage Auctions, which bills itself as “the world’s largest collectibles auctioneer,” had it splashed across the centerfold of its sale catalog. In midstride, with the mouth on the 4-foot-long skull gaping to show its spiky teeth, and its counterbalancing tail stretched out behind, Lot 49135 stood 8 feet tall and 24 feet long. The auction would take place that Sunday afternoon, just three days off, at a converted warehouse a short subway ride south of the museum. The estimate was that it would sell for $950,000 to $1.5 million. There was only one hitch:

Digging Out From the Ashes of a Ruined Museum

by Richard Conniff/Scientific American

With the hollowed-out shell of their old building standing in ruins nearby, and its history-rich contents in ashes, staff and scientists of Brazil’s National Museum met Wednesday morning for the first time since Sunday’s fire. They face a future suddenly bereft of a vast assortment of items from Brazil’s natural and cultural heritage, which explorers and researchers had collected and preserved over the museum’s 200-year history.

No one died or was injured in the fire—astonishingly, given staffers’ last-minute efforts to salvage specimens and equipment as parts of the building’s interior tumbled down around them. But one museum official estimated up to 18 million of the institution’s original 20 million specimens might have been destroyed in the raging blaze, which began soon after the building closed Sunday evening. Among the unique items missing and presumed lost were the only recordings of languages of tribes that have vanished, and the only specimens of plants and animals that have gone extinct, from places that in some cases no longer exist.

Museum Director Alexander Kellner told Scientific American that a meeting with members of Brazil’s congress, cabinet and Pres. Michel Temer had secured an immediate guarantee of $2.4 million to stabilize the museum’s gutted shell, located in a park on the north side of Rio de Janeiro, “and to recover what can be recovered.” This will inevitably be a slow process. Some paleontology specimens, for instance, may have survived within heavy-duty storage containers called compactors. But those compactors are now singed and covered with

Hello, My Name is Denisova 11. And Mom Is S-O-O-O-O Weird. Or Is It Dad?

Artist’s conception of a Neanderthal: This would be Denny’s mom.  (Photo: Joe McNally/National Geographic)

by Richard Conniff/Scientific American

In a remarkable twist in the story line of early human evolution, scientists have announced the discovery of “Denisova 11”—a female who was at least 13 years old, lived more than 50,000 years ago, and was the child of an early mixed marriage.

That is, her parents were not just of different races, but two different and now-extinct early human types. Their exact taxonomic designations—whether they were separate species or subspecies—is still a matter of scientific debate. But the bottom line for Denisova 11 is that mom was a Neandertal and dad was a Denisovan.

The research, published Wednesday in Nature, is the work of a team led by pioneering paleogeneticist Svante Pääbo at Max Planck Institute for Evolutionary Anthropology in Germany. He and his co-authors presented the first description of the Denisovans in 2010, based on genetic evidence from one of the 2,000 or so bone fragments found in Denisova Cave in the Altai Mountains,

The Telltale Bone, in 360 degrees (Photo Thomas Higham/Oxford University)

where Siberia borders Mongolia and China. The new discovery is based on another bone fragment from that lot, a 2.5-centimeter-long fragment of what was a femur or humerus, from which the researchers extracted six DNA samples and then cloned them for detailed analysis.

Molecular dating indicates that Denisovans, who are so far known only from Denisova Cave, and Neanderthals, known mainly from sites in Europe, diverged from each other almost 400,000 years ago. They coexisted, probably in relatively small populations scattered across the vast Eurasian landmass, until both became extinct some 30,000 to 40,000 years ago.

But the genetic evidence from Denisova 11 and other recent studies suggests that, on the occasions when they met, Denisovans and Neandertals commonly

Utah Yields a Giant Triassic Pterosaur–and It’s Largely Intact

 

Here’s the press release from Brigham Young University. (Sorry, didn’t have time to add it earlier.)  And small correction: Pterodactyl(us) is just a name for one genus of pterosaur, rather than a common name for all pterosaurs.

When Brooks Britt, a geological sciences professor at BYU, searched through the latest Triassic sandstone samples in his lab, he expected to find bones of early crocodiles and dinosaurs. Instead, he discovered the bones of a new pterosaur specimen, now named Caelestiventus (heavenly wind) hanseni. Dating back more than 200 million years, it’s one of the earliest ever found.

Until Britt’s discovery, newly published in the journal Nature Ecology and Evolution, there were only 30 known Triassic pterosaur (more commonly known as pterodactyl) specimens known to man — and none lived in deserts. Caelestiventus hanseni predates all desert pterosaurs by 65 million years. “We’re getting insights into the beginning of pterosaurs,” he said. “Ours shows that

India’s The Tiger Capital of the World. Here’s How It Could Do 5X Better

Sunderbans National Park, West Bengal, India (Photo: Soumyajit Nandy/ Wikimedia)

by Richard Conniff/Yale Environment 360

Ullas Karanth, a senior scientist with the Wildlife Conservation Society, is one of the world’s premier tiger experts and a leader in the effort to restore India’s depleted tiger populations. Raised in the South India state of Karnataka, he has spent much of his professional life studying and working to bring back tigers there, starting in Nagarahole National Park in the foothills of the Western Ghats, and then across a 10,000-square-mile region of that mountain range.

Karanth’s emphasis on scientific methods has frequently brought him into conflict with India’s forest bureaucracy, particularly over its insistence on estimating tiger populations based on footprint counts. Karanth instead pioneered the use of camera traps for population estimates based on identification of individual tigers. That method belatedly became the national standard after a 2004 scandal, when Sariska Tiger Reserve, officially estimated to have 26 tigers, turned out to have none.

Karanth’s willingness to report illegal logging, cattle grazing, and poaching in protected areas — and to implicate corrupt officials in the damage — has also earned him enemies. In one incident, an angry mob set a fire that destroyed his car, laboratory, and eight square miles of forest. But Karanth’s persistence has helped reestablish the tiger population in the Western Ghats and fueled his ambition to see that success extended across India and to empty tiger habitat far beyond.

Richard Conniff: India has managed to maintain a population of about 3,000 tigers for decades. What’s the potential population in a nation that’s also home to 1.3 billion people?

Ullas Karanth: There are at least 300,000 square kilometers of the type of forest in which tigers can live, which are still not converted to agriculture and which are under state ownership, protected as state-owned forest reserves. A subset of that, maybe 10 or 15 percent, is protected as wildlife reserves. So basically if all these 300,000 square kilometers were reasonably well protected and the prey base is brought up, we could have 10,000 to 15,000 tigers.

Conniff Is there any chance that that will happen?

Karanth: I don’t see why not. It’s essentially a function of

Acts of Gratitude: Remembering A Doctor’s Heroic Care

This morning I got word that Dr. Robert S. Modlinger, the endocrinologist who saved my life, has died at 72. Here is the obituary giving the considerable accomplishments of his career. But Bob Modlinger meant so much more than that to me and to so many other patients, despite his own disabling medical issues.

This is the column I wrote a few years ago to thank him.

BY RICHARD CONNIFF/The New York Times

JULY 5, 2007 6:53 PM

I’m too big a skeptic to put much faith in the circularity of life, with deeds done long ago coming round years later to haunt us or make us whole. But I began to think about the possibility recently, during a visit to Columbia University’s College of Physicians and Surgeons. One of the lectures that day was about the art of listening to patients’ stories with an almost literary ear, as a way of treating them with greater insight and sensitivity.

The speaker was looking at things only from the doctor’s perspective. But it struck me that there are at least two sides to every medical story. And it got me thinking back 30 years, to when I was a young man dying of no apparent cause.

My symptoms then included listlessness, faint-headedness, an inability to climb stairs without resting and unquenchable thirst. Twice, I took home a jug for a 24-hour urine test, and both times I came back with an extra bottle on the side. It didn’t seem to signify much to my doctor. The heart was his specialty, and he kept doing electrocardiograms suggesting something wrong there, but no particular diagnosis. I wasn’t much interested, in any case. I was only 26 years old, but the idea of dying seemed perfectly fine.

Then one afternoon

A Probiotic Vaccine Aims to Stop Cholera Epidemics Fast

by Richard Conniff/Scientific American

The most terrifying things about cholera is its lethal speed. A victim can consume contaminated food or water, come down with diarrhea a day later and, if untreated, be dead a day after that—having inadvertently spread the microorganism to friends, neighbors and family members in the meantime. Hence cholera’s reputation for tearing explosively through populations, mostly recently in Haiti beginning in 2010 and Yemen in 2016.

Two major challenges—one diagnostic, the other preventive—make it difficult to stop cholera epidemics: A simple field test can distinguish cholera from other forms of diarrhea, but only after symptoms have already appeared. And although existing vaccines can prevent the disease, they require two or three weeks to elicit protective immunity. Neither diagnosis nor vaccination is fast enough for public health workers racing to stop the first few cases of cholera from breaking out into an epidemic.

Two new studies published this month in Science Translational Medicine could change that, although both are still in preliminary testing on animal models of cholera. In the first study researchers at Massachusetts Institute of Technology wanted to know “whether we could engineer a bacterium that could serve both to diagnose and prevent cholera,” says senior author James Collins. The researchers focused on Lactococcus lactis, which people have routinely consumed for thousands of years incultured dairy products like yogurt and sour cream.

The initial plan for treatment was to genetically engineer the bacterium “to produce and secrete antimicrobial peptides specific to cholera,” Collins says. But on attempting to culture L. lactis in a laboratory dish together with the cholera pathogen, he says, the researchers found to their “pleasant surprise” that no such engineering was needed: L. lactis “was either inhibiting or killing off the cholera” on its own. This was apparently because the lactic acid it secretes creates an inhospitable environment for the cholera pathogen in the petri dish—as it also presumably does in the small intestine. In testing on laboratory mice 84.6 percent of those fed L. lactis and the cholera pathogen together survived, compared with 45.7 percent of those fed the cholera pathogen alone. When the researchers experimentally altered L. lactis to stop it from producing lactic acid, this protective effect disappeared. It was, Collins says, the first time anyone has demonstrated

Selling the Protected Area Myth (No Wildlife Need Apply)

Chevron’s Gas Plant Being Built in a Class A Protected Area

by Richard Conniff/The New York Times

It’s widely celebrated as one of the few success stories in the push to protect the wildlife we claim to love: Since the early 1990s, governments have roughly doubled the extent of natural areas under protection, with almost 15 percent of the terrestrial Earth and perhaps 5 percent of the oceans now set aside for wildlife. From 2004 to 2014, nations designated an astonishing 43,000 new protected areas.

These numbers are likely to increase, as the 168 nations that are signatories to the 1993 Convention on Biological Diversity work to meet their target of 17 percent terrestrial and 10 percent marine protected area coverage by 2020. And at that point, even more ambitious targets should kick in.

So, hurrah, right?

Sadly, there are two big delusions at work here. The first is that designating protected areas is

When We Protect “Umbrella Species,” Who Else Gets In Under The Umbrella?

Sage-grouse (Photo: Dave Showalter)

by Richard Conniff/Yale Environment 360

Conservationists often criticize state fish and game departments for focusing single-mindedly on one species to the detriment of everything else — for instance, improving habitat for elk, which then browse down habitat for songbirds. But what if conservationists — who don’t have that traditional hook-and-bullet mindset — nonetheless inadvertently do much the same thing?

That’s one implication of new research looking at the umbrella species concept, one of the fundamental ideas driving conservation efforts worldwide. It’s the idea routinely advocated by conservationists that establishing and managing protected areas for the benefit of one surrogate species — from gorillas to grizzly bears — will also indirectly benefit a host of other, less charismatic species sharing the same habitat. “The umbrella species concept is an appealing shortcut,” says Jason Carlisle, who conducted the research as a doctoral candidate at the University of Wyoming.  But the complications quickly pile up.

Across much of the American West, the greater sage grouse is one such umbrella species. It’s widely considered (but not officially listed as) an endangered species, with a population down from millions of individuals across 16 states and three Canadian provinces a century ago to fewer than 400,000 in a sharply reduced and fragmented range today.

In 2015, an unprecedented consortium of states, federal agencies, private landowners, industry, and environmentalists agreed to a painstakingly negotiated collaboration to protect the sage grouse and to make it an umbrella for 350 other “background” species in sagebrush habitat. Then, last August the Trump Administration threw out that Obama-era agreement and reopened sage grouse habitat on federal lands to additional mining, drilling, cattle grazing, and off-road vehicle use — all factors that helped imperil sage grouse in the first place.

In reality, Carlisle and his co-authors suggest, the protective umbrella created under the 2015 agreement should have been