As Quakes Rattle Oklahoma, Fingers Point to Oil and Gas Industry

PRAGUE, Okla. — Yanked without warning from a deep sleep, Jennifer Lin Cooper, whose family has lived near here for more than a half-century, could think only that the clamor enveloping her house was coming from a helicopter landing on her roof. She was wrong.

A 5.0-magnitude earthquake — the first of three as strong or stronger over several days in November 2011 — had peeled the brick facade from the $117,000 home she bought the year before. Ms. Cooper, 36, could not get out until her father pried a stuck storm door off the front entrance. Repairs have so far cost $12,000 and forced her to take a second job, at night, to pay the bill.

At a packed town hall meeting days later, Ms. Cooper said, state officials called the shocks, including a 5.7 tremor that was Oklahoma’s largest ever, “an act of nature, and it was nobody’s fault.”

Many scientists disagree. They say those quakes, and thousands of others before and since, are mainly the work of humans, caused by wells used to bury vast amounts of wastewater from and gas exploration deep in the earth near fault zones. And they warn that continuing to entomb such huge quantities risks more dangerous tremors — if not here, then elsewhere in the state’s sprawling well fields.

“As long as you keep injecting wastewater along that fault zone, according to my calculations, you’re going to continue to have earthquakes,” said Arthur F. McGarr, the chief of the induced seismicity project at the federal Earthquake Science Center in Menlo Park, Calif., who has . “I’d be a little worried if I lived there. In fact, I’d be very worried.”

But in a state where and gas are economic pillars, elected leaders have been slow to address the problem. And while regulators have taken some protective measures, they lack the money, work force and legal authority to fully address the threats.

More than five years after the quakes began a sharp and steady increase, the strongest action by the Republican governor, Mary Fallin, has been to name a council to exchange information about the tremors. The group meets in secret, and has no mandate to issue recommendations.

The State Legislature is not considering any earthquake legislation. But both houses passed bills this year barring local officials from regulating oil and gas wells in their jurisdictions.

The state seismologist’s office, short-staffed, has stopped analyzing data on tremors smaller than magnitude 2.5 — even though says those quakes flag hidden seismic hazards “that might prove invaluable for avoiding a damaging earthquake.”

The governor referred an interview request to Michael Teague, her energy and environment secretary. Mr. Teague said the governor’s earthquake council was helping coordinate the response to the shocks and that underfunded regulators and scientists had benefited from efforts to find new state and federal assistance for their work.

“It’s not working well enough if your house is shaking, absolutely no doubt,” he said. “But it’s working very well.”

But others say the political will is missing to confront an earthquake threat tied to Oklahoma’s dominant industry.

It is “a dangerous game of Russian roulette,” said Jason Murphey, the Republican state representative from earthquake-ridden Guthrie, in central Oklahoma. “If a dangerous earthquake happens and causes lots of damage and injuries,” he said, “a cloud will hang over the energy sector for a long time to come.”

If scientists see dangers, many Oklahomans are wary of disrupting an industry so woven into everyday life.

The state’s oil and gas wells gush profits to corporate owners, but also royalties to farmers and homeowners, and tax payments to the state and cities. By some accounts the industry supports as many as one in five Oklahoma jobs. It showers Oklahoma universities with millions of dollars in donations and helps make dreams like Oklahoma City’s N.B.A. franchise, reality.

It is also a major political contributor to Ms. Fallin, legislators and all three elected members of the , which oversees oil and gas production and disposal wells.

“We always want to be invited to the prom,” said State Representative Cory Williams, a Democrat from Stillwater, the home of Oklahoma State University and one of the state’s most seismically active areas. “And we’ve decided that oil and gas is the best prom date we’ll ever get, and we don’t want oil and gas to go away.”

Those blessings, however, are not unalloyed.

From 2010 to 2013, Oklahoma oil production jumped by two-thirds and gas production rose by more than one-sixth, federal figures show. The amount of wastewater buried annually rose one-fifth, to nearly 1.1 billion barrels. And Oklahoma went from three earthquakes of magnitude 3.0 or greater to 109 — and to 585 in 2014, and to 750-plus this year, should the current pace continue. In the United States, only Alaska is shaken more.

The Corporation Commission lacks explicit authority to regulate earthquake risks. So it is trying to contain the risks posed by roughly 3,200 active wastewater disposal wells using laws written to control water pollution.

Last spring, the commission began trying to weed out quake risks by scrutinizing wells near larger quakes for operational problems and permit violations. A few dozen wells made modifications; four shut down. It is now difficult to win approval for new wells near stressed faults, active seismic areas or the epicenters of previous quakes above 4.0 magnitude. Regulators significantly expanded the areas under scrutiny last month. Yet the quakes continue.

Privately, some companies are cooperating with regulators and scientists by offering proprietary information about underground faults. Publicly, the industry wants Oklahomans to beware of killing the golden goose.

Many in the industry were reluctant to comment for this article. But Kim Hatfield, the regulatory chairman of the and president of Crawley Petroleum, warned: “A reaction of panic is not useful.”

Shutting down disposal wells and the industry they serve, he added, “will make look like a cheery movie.”

The mechanics of wastewater-induced earthquakes are straightforward: Soaked with enough fluid, a layer of rock expands and gets heavier. Earthquakes can occur when the pressure from the fluid reaches a fault, either through direct contact with the soaked rock or indirectly, from the expanding rock. Seismologists have documented such quakes in , New Mexico, , Kansas and elsewhere since the 1960s.

But nowhere have they approached the number and scope of Oklahoma’s quakes, which have rocked a fifth of the state. One reason, scientists suspect, is that Oklahoma’s main waste disposal site, a bed of porous limestone thousands of feet underground, lies close to the hard, highly stressed rock containing the faults that cause quakes.

The salty, sometimes toxic wastewater is a byproduct of extracting oil and gas, whether by hydraulic fracturing of once-unreachable shale deposits, commonly called fracking, or from conventional wells. Most is pumped out of the ground with oil or gas, then returned to the earth in a so-called disposal well, often at a different location.

The Corporation Commission faces a complicated task. It can order a shutdown or operational change only one well at a time, and only if a well violates its operating permit or is clearly tied to an earthquake risk.

But geologists say the sheer volume of waste being buried in an area with many wells — and not any single well — causes most quakes. It often is difficult or impossible to assess blame to a particular well.

Some other states like Arkansas and, this week, , have imposed blanket shutdowns or cutbacks on wells near active quake zones. “We don’t have the ability or the legal authority to issue a moratorium,” Dana Murphy, one of the three elected corporation commissioners, said in an interview.

“We do have the ability to take certain actions in emergency situations,” she continued. “But that’s emergencies when they start happening. It doesn’t talk about what happens before the emergencies occur.”

The 2011 quakes that damaged Ms. Cooper’s home in Prague (pronounced “prayg”) illustrate the regulators’ limited reach.

Acting on geologists’ suspicions after the first temblor, regulators tested and pored over operations data from three wells — two small ones and a huge one, called Wilzetta, sunk by the Tulsa-based company New Dominion in 1999. They were seeking some definitive cause of the tremor.

They found none. The wells still pump today, even as worried regulators wave off operators who want to sink new ones. Indeed, by December 2013, Wilzetta had nearly doubled its average monthly volume of waste compared with the months before the 2011 shocks.

Without convincing evidence that a well poses a seismic threat, one official said, regulators are powerless to order precautions, much less shutdowns. “Shut it in? How?” said that official, who spoke on the condition of anonymity because he was barred from discussing specific cases. “Show me the cause. Show me the violation.”

Hamstrung, regulators now may have pushed their authority to its limits. Beginning last May, the commission began tightening permits for new disposal wells, requiring seismicity tests and requiring shutdowns if quakes occurred nearby.

Existing wells were unaffected. But last month the agency required operators of hundreds of wells to prove they were not accidentally pumping wastewater into bedrock, which seismologists say raises earthquake risks.

“We are operating on the assumption that time is of the essence,” a regulatory program manager at the commission, Matt Skinner, said in an interview.

Scientists certainly agree.

Federal seismologists have for a year warned of rising earthquake risks. Last July, that wastewater-induced earthquakes were approaching a fault near Oklahoma City capable of producing a magnitude 7.0 shock, though other experts call that unlikely. In January, scientists including Oklahoma’s state seismologist, Austin Holland, and identified three faults capable of “significantly larger” earthquakes.

Last month, a South African geophysicist delivered : Another magnitude 5-plus quake could occur by 2016, and one fault running through Stillwater and two other cities potentially could yield up to a magnitude 6.5 shock.

While scientists worry, political leaders have been slow to recognize the threat.

First elected in 2010, Governor Fallin appointed the earthquake advisory council last September. “Oklahoma has always had seismic activity, but the reality is we are seeing more,” she said then. “It’s important that we study this issue and have sound science that can inform decisions.”

She allowed only last week that wells accidentally drilled into rock containing faults could “potentially” set off shocks. Scientists say that is only one factor at play in the quakes.

The governor’s 12-member earthquake advisory council, drawn from industry, government, the Legislature and academia, works as an information clearinghouse, said Mr. Teague, her energy and environment secretary and the group’s chairman.

“The whole idea of the group,” he said, “is what are you working on? What are the gaps that you’ve got, and is there somebody else that can fill that gap?”

The most glaring gaps, however, remain mostly unfilled.

Last month the state promised a clerk, two technical experts and $50,000 to help regulators assess wells, but a $600 million-plus budget deficit makes significant aid unlikely. The Legislature could grant the commission greater authority, but legislators say that is not an option in a state where regulation is deeply unpopular, and the oil and gas industry holds political and economic sway.

The industry has worked on several fronts to contain concern about the quakes.

In October 2013, almost two years after the Prague quakes, Dr. Holland, the state seismologist, issued a news release warning that the earthquake risk in Oklahoma City, about 50 miles west of Prague, had increased. Wastewater disposal wells, he added, may be “a contributing factor.” Two weeks later, he was summoned to the office of the University of Oklahoma’s president, David L. Boren, to meet Harold G. Hamm, the chairman of Continental Resources, one of the state’s biggest oil and gas companies. Mr. Boren sits on Continental’s board, for which he has been paid more than $1.6 million in stock awards and directors’ fees since 2009, according to proxy statements.

Continental officials did not respond to a request for comment. Last month, after the newsletter reported the meeting, Mr. Boren called the session “purely informational.”

Dr. Holland said that Mr. Boren assured him his academic freedom as a scientist was unchallenged. Then, Dr. Holland said, Mr. Hamm told him that public discussions of disposal wells “are unnerving — they can dramatically affect the industry.”

Continental is seeking to shape that public discussion, arguing , and that the earthquake epidemic is not man-made, but part of an unusually active period for quakes worldwide.

and in courtrooms, some residents have begun to demand an accounting. In August, Sandra Ladra, a Prague resident injured by a collapsing fireplace during the 2011 earthquakes, sued the Wilzetta well’s operator, New Dominion, and the Spess Oil Company, which operates the two smaller wells nearby.

Then, in February, came a class-action lawsuit against the two companies by Ms. Cooper, whose house in Prague was heavily damaged. Her suit seeks compensation for quake damage not only to her home, but to any homes in nine counties surrounding Prague.

That case has yet to be heard. But Ms. Ladra’s suit, now before the State Supreme Court, previews the industry response: The wells operate legally, and regulators should hear complaints against them. Letting juries decide their culpability in earthquakes invites financial disaster.

“I don’t want to belittle the public’s concern about earthquake swarms. I live here, too,” Robert G. Gum, a lawyer for New Dominion, said at an October hearing. “But it’s no more important to the people sitting in this courtroom and the people in this state than the state’s economy. It’s no more important in recognizing how important the oil and gas industry is to that economy.”

If juries hold the companies liable for Prague’s earthquakes, he added, “I doubt if this is the last lawsuit that will get filed. These wells will become economic and legal liability pariahs. They will be shut down.”

To Ms. Cooper, that message is clear. “People need to just take their losses for the greater good of the oil and gas companies — you know, do your part,” she said.

She does not buy it.

“If the truth destroys something,” she said, “then it needs to be destroyed.”

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Nuclear Plant in Iranian Desert Emerges as Flash Point in Talks

The site looms up from the Iranian desert like something out of a thriller novel, ringed by antiaircraft batteries, a security perimeter two miles around, and huge tunnels that lead deep into the mountainous complex.

Welcome to Fordo. Once a covert site of ’s sprawling , then a closely monitored uranium enrichment plant, it is now a flash point in this week’s preliminary nuclear deal between the West and Tehran. The question is whether the proposed conversion of the site to a peaceful research center will prove effective or instead produce an illusion that eventually aids Iran’s pursuit of an atom bomb.

Fordo — some 20 miles from the holy city of Qum, deep inside an Iranian Revolutionary Guards base — came to public attention in 2009 when .

The secret plant, Mr. Obama said, “represents a direct challenge to the basic foundation of the nonproliferation regime.” The Iranians, he added, “are going to have to come clean.”

The Nonproliferation Treaty allows no secret work that could have application to the making of nuclear warheads. But inspectors from the International Atomic Energy Agency soon discovered that the Iranians planned to fill the cavernous halls with row upon row of centrifuges — tall machines that spin very fast to concentrate the rare form of uranium that fuels reactors and bombs.

By late 2011, Iran had installed hundreds of centrifuges at Fordo and had begun enriching uranium to 20 percent, just shy of bomb purity. By 2012, the number of centrifuges at the underground plant had soared to more than 2,700, though only 696 were in use.

The deep site represented a bold move in Iran’s war of nerves with the West. So much rock covered the enrichment halls that they could withstand all but the most powerful bombs. And Tehran, whenever it wanted, could throw another 2,000 centrifuges into enrichment.

In 2012, at the United Nations, Prime Minister Benjamin Netanyahu of Israel identified a “red line” beyond which he said Iran must not be allowed to pass: when it had enough purified uranium to quickly make a single nuclear weapon.

Fordo is buried in a mountain deep inside an Islamic Revolutionary Guards Corps base. The site came to public attention in 2009 when President Obama announced its existence.

Caspian

Sea

FORDO

Tehran

Fordo

Natanz

Arak

Tunnel entrances

IRAQ

IRAN

Persian

Gulf

SAUDI

ARABIA

QATAR

200 miles

FORDO

Tunnel entrances

Caspian

Sea

Tehran

Fordo

IRAQ

Natanz

Arak

IRAN

Persian

Gulf

200 miles

SAUDI ARABIA

Source: Satellite photograph by Google (2013).

By The New York Times

In late 2013, the negotiations began on limiting Iran’s nuclear program and lifting economic sanctions, and Tehran agreed to stop purifying uranium to 20 percent at Fordo, immediately reducing the danger of rapidly crossing the red line. Instead, enrichment would be kept to less than 5 percent, a concentration often used in generating electricity.

Many nuclear experts and American officials expected that the negotiations would end with Fordo’s complete dismantlement. David Albright, the president of the Institute for Science and International Security, a Washington research group that monitors , that “a key demand will be that this site close down.”

But the preliminary deal announced in Switzerland on Thursday instead calls for the site’s conversion exclusively to peaceful research. Iran has agreed to forgo enriching uranium at Fordo for at least 15 years, and to conduct no research there on new enrichment gear. The proposed deal also calls for the removal of “almost two-thirds of Fordo’s centrifuges and infrastructure.”

R. Scott Kemp, a centrifuge expert at M.I.T. who formerly worked at the State Department and Princeton, hailed the overall deal as “a remarkable achievement” but said Fordo could be a spoiler.

Since the deal allows the retention of roughly 1,000 centrifuges in the site’s underground halls, and says nothing about forbidding the installation of highly advanced ones so long as they do no uranium enrichment, the site might eventually pose a danger, Dr. Kemp on the website of the M.I.T. Laboratory for Nuclear Security and Policy.

He said Fordo thus configured might enable Iran to acquire the fuel for a bomb in as little as three months; the Obama administration has sought to lengthen the so-called breakout time to at least one year.

The retained centrifuges, Dr. Kemp wrote, “could be rapidly repurposed for enriching uranium under a breakout scenario” unless they were specifically designed to be incompatible with such purification.

He said that between now and late June, when negotiators are to complete the nuclear accord, they will face “the difficult task” of ensuring that centrifuges at Fordo are “physically incapable of uranium enrichment.”

An alternative, he added, would be restrictions on the number and type of centrifuges allowed.

“If this oversight is addressed,” Dr. Kemp said, the rest of the deal would “lengthen the breakout time to about one year.”

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Women Are Less Likely to Harm One Person To Help Many

Crying Baby

You are hiding from enemy soldiers when an orphaned baby begins to cry. Do you smother the baby, if it's the only way to save yourself and the others from the enemy from being captured? What if you will all be killed if you don't?

In the face of such a brain-scrambling, gut-wrenching scenario, published today in the Society for Personality and Social Psychology Bulletin found, women are less likely than men to take the harmful action, even if for the sake of the greater good.

The study, led by researchers at Wilfrid Laurier University in Ontario, Canada, the University of Cologne, and the University of Texas at Austin, analyzed 40 previous studies that together asked 6,100 men and women the choices they would make when confronted with 10 moral quandaries related to murder, torture, lying, abortion, and animal research. All pitted two ethical philosophies against each other: deontology and utilitarianism. Deontology takes a do-no-harm approach to ethics: an action is either morally right or wrong, no matter its consequences. Utilitarianism, on the other hand, holds that an action is moral if it results in the greatest good for the most people.

Based on participants’ patterns of response, researchers developed an algebraic equation to quantify the strength of deontological and utilitarian inclinations among men and women. They found that only 54 percent of women would make a utilitarian choice--like smothering the crying baby in the example above--if it meant minimizing harm to others, compared with 64 percent of men.

When researchers further examined these choices, they found no evidence that differences exist when it comes to how men and women rationally evaluate an outcome of taking a utilitarian action. Instead, researchers found that the gender difference in moral decisions is caused by a stronger gut-level reaction among women than among men to causing harm to others.

“Both men and women are governed by intellect when it comes to making tough choices. Women additionally experience a strong emotional response that informs their decision.” said Rebecca Friesdorf, a graduate student in social psychology at the Wilfrid Laurier University, and the lead author of the study.

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Is Most of Our DNA Garbage?

T. Ryan Gregory’s lab at the University of Guelph in Ontario is a sort of genomic menagerie, stocked with creatures, living and dead, waiting to have their DNA laid bare. Scorpions lurk in their terrariums. Tarantulas doze under bowls. Flash-frozen spiders and crustaceans — collected by Gregory, an evolutionary biologist, and his students on expeditions to the Arctic — lie piled in beige metal tanks of liquid nitrogen. A bank of standing freezers holds samples of mollusks, moths and beetles. The cabinets are crammed with slides splashed with the fuchsia-stained genomes of fruit bats, Siamese fighting fish and ostriches.

Gregory’s investigations into all these genomes has taught him a big lesson about life: At its most fundamental level, it’s a mess. His favorite way to demonstrate this is through what he calls the “onion test,” which involves comparing the size of an onion’s genome to that of a human. To run the test, Gregory’s graduate student Nick Jeffery brought a young onion plant to the lab from the university greenhouse. He handed me a single-edged safety razor, and then the two of us chopped up onion stems in petri dishes. An emerald ooze, weirdly luminous, filled my dish. I was so distracted by the color that I slashed my ring finger with the razor blade, but that saved me the trouble of poking myself with a syringe — I was to supply the human genome. Jeffery raised a vial, and I wiped my bleeding finger across its rim. We poured the onion juice into the vial as well and watched as the green and red combined to produce a fluid with both the tint and viscosity of maple syrup.

After adding a fluorescent dye that attaches to DNA, Jeffrey loaded the vial into a boxy device called a flow cytometer, which sprayed the onion juice and blood through a laser beam. Each time a cell was hit, its DNA gave off a bluish glow; bigger genomes glowed more brightly. On a monitor, we watched the data accumulate on a graph. The cells produced two distinct glows, one dim, one bright, which registered on the graph as a pair of peaks.

One peak represented my genome, or the entirety of my DNA. Genomes are like biological books, written in genetic letters known as bases; the human genome contains about 3.2 billion bases. Print them out as letters on a page, and they would fill a book a thousand times longer than “War and Peace.” Gregory leaned toward the screen. At 39, with a chestnut-colored goatee and an intense gaze, he somewhat resembles a pre-Heisenberg Walter White. He pointed out the onion’s peak. It showed that the onion’s genome was five times bigger than mine.

“The onion wins,” Gregory said. The onion always does.

But why? Why does an onion carry around so much more genetic material than a human? Or why, for that matter, do the broad-footed salamander (65.5 billion bases), the African lungfish (132 billion) and the (149 billion)? These organisms don’t appear to be more complex than we are, so Gregory rejects the idea that they’re accomplishing more with all their extra DNA. Instead, he champions an idea first developed in the 1970s but still startling today: that the size of an animal’s or plant’s genome has essentially no relationship to its complexity, because a vast majority of its DNA is — to put it bluntly — junk.

The human genome contains around 20,000 genes, that is, the stretches of DNA that encode proteins. But these genes account for only about 1.2 percent of the total genome. The other 98.8 percent is known as noncoding DNA. Gregory believes that while some noncoding DNA is essential, most probably does nothing for us at all, and until recently, most biologists agreed with him. Surveying the genome with the best tools at their disposal, they believed that only a small portion of noncoding DNA showed any evidence of having any function.

But in the past few years, the tide has shifted within the field. Recent studies have revealed a wealth of new pieces of noncoding DNA that do seem to be as important to our survival as our more familiar genes. Many of them may encode molecules that help guide our development from a fertilized egg to a healthy adult, for example. If these pieces of noncoding DNA become damaged, we may suffer devastating consequences like brain damage or cancer, depending on what pieces are affected. Large-scale surveys of the genome have led a number of researchers to expect that the human genome will turn out to be even more full of activity than previously thought.

In January, Francis Collins, the director of the National Institutes of Health, made a comment that revealed just how far the consensus has moved. At a health care conference in San Francisco, an audience member asked him about junk DNA. “We don’t use that term anymore,” Collins replied. “It was pretty much a case of hubris to imagine that we could dispense with any part of the genome — as if we knew enough to say it wasn’t functional.” Most of the DNA that scientists once thought was just taking up space in the genome, Collins said, “turns out to be doing stuff.”

For Gregory and a group of like-minded biologists, this idea is not just preposterous but also perilous, something that could yield bad science. The turn against the notion of junk DNA, they argue, is based on overinterpretations of wispy evidence and a willful ignorance of years of solid research on the genome. They’ve challenged their opponents face to face at scientific meetings. They’ve written detailed critiques in biology journals. They’ve commented on social media. When the N.I.H.’s official Twitter account relayed Collins’s claim about not using the term “junk DNA” anymore, Michael Eisen, a professor at the University of California, Berkeley, tweeted back with a profanity.

The junk DNA wars are being waged at the frontiers of biology, but they’re really just the latest skirmish in an intellectual struggle that has played out over the past 200 years. Before Charles Darwin articulated his theory of evolution, most naturalists saw phenomena in nature, from an orchid’s petal to the hook of a vulture’s beak, as things literally designed by God. After Darwin, they began to see them as designs produced, instead, by natural selection. But some of our greatest biologists pushed back against the idea that everything we discover in an organism had to be an exquisite adaptation. To these biologists, a fully efficient genome would be inconsistent with the arbitrariness of our genesis, with the fact that every species emerged through pure happenstance, over eons of false starts. Where some look at all those billions of bases and see a finely tuned machine, others, like Gregory, see a disorganized, glorious mess.

n 1953, Francis Crick and James Watson published a short paper in the journal Nature setting out the double-helix structure of DNA. That brief note sent biologists into a frenzy of discovery, leading eventually to multiple Nobel Prizes and to an unprecedented depth of understanding about how living things grow and reproduce. To make a protein from DNA, they learned, a cell makes a single-stranded copy of the relevant gene, using a molecule called RNA. It then builds a corresponding protein using the RNA as a guide.

This research led scientists to assume that the genome was mostly made up of protein-coding DNA. But eventually scientists found this assumption hard to square with reality. In 1964, the German biologist Friedrich Vogel did a rough calculation of how many genes a typical human must carry. Scientists had already discovered how big the human genome was by staining the DNA in cells, looking at the cells through microscopes and measuring its size. If the human genome was made of nothing but genes, Vogel found, it would need to have an awful lot of them — 6.7 million genes by his estimate, a number that, when he published it in Nature, he admitted was “disturbingly high.” There was no evidence that our cells made 6.7 million proteins or anything close to that figure.

Vogel speculated that a lot of the genome was made up of essential noncoding DNA — possibly operating as something like switches, for example, to turn genes on and off. But other scientists recognized that even this idea couldn’t make sense mathematically. On average, each baby is born with roughly 100 new mutations. If every piece of the genome were essential, then many of those mutations would lead to significant birth defects, with the defects only multiplying over the course of generations; in less than a century, the species would become extinct.

Faced with this paradox, Crick and other scientists developed a new vision of the genome during the 1970s. Instead of being overwhelmingly packed with coding DNA, the genome was made up mostly of noncoding DNA. And, what’s more, most of that noncoding DNA was junk — that is, pieces of DNA that do nothing for us. These biologists argued that some pieces of junk started out as genes, but were later disabled by mutations. Other pieces, called transposable elements, were like parasites, simply making new copies of themselves that were usually inserted harmlessly back in the genome.

Junk DNA’s recognition was part of a bigger trend in biology at the time. A number of scientists were questioning the assumption that biological systems are invariably “well designed” by evolution. In a 1979 paper in The Proceedings of the Royal Society of London, Stephen Jay Gould and Richard Lewontin, both of Harvard, groused that too many scientists indulged in breezy storytelling to explain every trait, from antlers to jealousy, as an adaptation honed by natural selection for some essential function. Gould and Lewontin refer to this habit as the Panglossian paradigm, a reference to Voltaire’s “Candide,” in which the foolish Professor Pangloss keeps insisting, in the face of death and disaster, that we live in “the best of all possible worlds.” Gould and Lewontin did not deny that natural selection was a powerful force, but they stressed that it was not the only explanation for why species are the way they are. Male nipples are not adaptations, for example; they’re just along for the ride.

Gould and Lewontin called instead for a broader vision of evolution, with room for other forces, for flukes and historical contingencies, for processes unfolding at different levels of life — what Gould “pluralism.” At the time, geneticists were getting their first glimpses of the molecular secrets of the human genome, and Gould and Lewontin saw more evidence for pluralism and against the Panglosses. Any two people may have millions of differences in their genomes. Most of those differences aren’t a result of natural selection’s guiding force; they just arise through random mutations, without any effect for good or ill.

When Crick and others began to argue for junk DNA, they were guided by a similar vision of nature as slipshod. Just as male nipples are a useless vestige of evolution, so, in their theory, is a majority of our genome. Far from the height of machine-like perfection, the genome is largely a palimpsest of worthless instructions, a den of harmless parasites. Crick and his colleagues argued that transposable elements were common in our genome not because they did something essential for us, but because they could exploit us for their own replication. Gould delighted at this good intellectual company, arguing that transposable elements behaved like miniature organisms, evolving to become better at adding new copies to their host genomes. Our genomes were their ocean, their savanna. “They are merely playing Darwin’s game, but at the ‘wrong level,’ ” Gould wrote in 1981.

Soon after Gould wrote those words, scientists set out to decipher the precise sequence of the entire human genome. It wasn’t until 2001, shortly before Gould’s death, that they published their first draft. They identified thousands of segments that had the hallmarks of dead genes. They found transposable elements by the millions. The Human Genome Project team declared that our DNA consisted of isolated oases of protein-coding genes surrounded by “vast expanses of unpopulated desert where only noncoding ‘junk’ DNA can be found.” Junk DNA had started out as a theoretical argument, but now the messiness of our evolution was laid bare for all to see.

see the genome in a fundamentally different way, the best place to go is the third floor of Harvard’s Department of Stem Cell and Regenerative Biology, in a maze of cluttered benches, sequencing machines and microscopes. This is the lab of John Rinn, a 38-year-old former competitive snowboarder who likes to ponder biological questions on top of a skateboard, which he rides from one wall of his office to the other and back. Rinn is overseeing more than a dozen research projects looking for pieces of noncoding DNA that might once have been classified as junk but actually are essential for life.

Rinn studies RNA, but not the RNA that our cells use as a template for making proteins. Scientists have long known that the human genome contains some genes for other types of RNA: strands of bases that carry out other jobs in the cell, like helping to weld together the building blocks of proteins. In the early 2000s, Rinn and other scientists discovered that human cells were reading thousands of segments of their DNA, not just the coding parts, and producing RNA molecules in the process. They wondered whether these RNA molecules could be serving some vital function.

As a postdoctoral fellow at Stanford University, Rinn decided he would try to show that one of these new RNA molecules had some important role. After a couple years of searching, he and a professor there, Howard Chang, settled on an RNA molecule that, somewhat bizarrely, was produced widely by skin cells below the waist but not above. Rinn and Chang were well aware that this pattern might be meaningless, but they set out to investigate it nevertheless. They had to give their enigmatic molecule a name, so they picked one that was a joke at their own expense: hotair. (“If it ends up being hot air, at least we tried,” Rinn said.)

Rinn ran a series of experiments on skin cells to figure out what, if anything, hotair was doing. He carefully pulled hotair molecules out of the cells and examined them to see if they had attached to any other molecules. They had, in fact: they were stuck to a protein called Polycomb.

Polycomb belongs to a group of proteins that are essential to the development of animals from a fertilized egg. They turn genes on and off in different patterns, so that a uniform clump of cells can give rise to bone, muscle and brain. Polycomb latches onto a number of genes and muzzles them, preventing them from making proteins. Rinn’s research revealed that hotair acts as a kind of guide for Polycomb, attaching to it and escorting it through the jungle of the cell to the precise spots on our DNA where it needs to silence genes.

When Rinn announced this result in 2007, other geneticists were stunned. Cell, the journal that released it, , calling Rinn’s paper one of the most important they had ever published. In the years since, Chang and other researchers have continued to examine hotair, using even more sophisticated tools. They bred engineered mice that lack the hotair gene, for example, and found that the mice developed a constellation of deformities, like stunted wrists and jumbled vertebrae. It appears very likely that hotair performs important jobs throughout the body, not just in the skin but in the skeleton and in other tissues too.

In 2008, having been lured to Harvard, Rinn set up his new lab entirely in hopes of finding more hotair-like molecules. The first day I visited, a research associate named Diana Sanchez was dissecting mouse embryos the size of pinto beans. In a bowl of ice next to her were tubes for the parts she delicately removed — liver, leg, kidney, lung — that would be searched for cells making RNA molecules. After Rinn and I left Sanchez to her dissections, we ran into Martin Sauvageau, a blue-eyed Quebecer carrying a case of slides, each affixed with a slice of a mouse’s brain, with stains revealing cells making different RNA molecules. I tagged along with Sauvageau as he headed to a darkened microscope room to look at the slides with a pink-haired grad student named Abbie Groff. On one slide, a mouse’s brain looked as if it wore a cerulean mustache. To Groff, every pattern comes as a surprise. She once discovered an RNA molecule that created thousands of tiny rings on a mouse’s body, each encircling a hair follicle. “You come in in the morning, and it’s like Christmas,” she said.

In December 2013, Rinn and his colleagues published the first results of their search: three potential new genes for RNA that appear to be essential for a mouse’s survival. To investigate each potential gene, the scientists removed one of the two copies in mice. When the mice mated, some of their embryos ended up with two copies of the gene, some with one and some with none. If these mice lacked any of these three pieces of DNA, they died in utero or shortly after birth. “You take away a piece of junk DNA, and the mouse dies,” Rinn said. “If you can come up with a criticism of that, go ahead. But I’m pretty satisfied. I’ve found a new piece of the genome that’s required for life.”

As the scientists find new RNA molecules that look to be important, they are picking out a few to examine in close molecular detail. “I’m totally in love with this one,” Rinn said, standing at a whiteboard wall and drawing a looping line to illustrate yet another RNA molecule, one that he calls “firre.” The experiments that Rinn’s team has run on firre suggest that it performs a spectacular lasso act, grabbing onto three different chromosomes at once and drawing them together. Rinn suspects that there are thousands of RNA molecules encoded in our genomes that perform similar feats: bending DNA, unspooling it, bringing it in contact with certain proteins and otherwise endowing it with a versatility it would lack on its own.

“It’s genomic origami,” Rinn said about this theory. “In every cell, you have the same piece of paper. Stem cell, brain cell, liver cell, it’s all made from the same piece of paper. How you fold that paper determines if you get a paper airplane or a duck. It’s the shape that you fold it into that matters. This has to be the 3-D code of biology.”

, discoveries like Rinn’s hint at a hidden treasure house in our genome. Because a few of these RNA molecules have turned out to be so crucial, they think, the rest of the noncoding genome must be crammed with riches. But to Gregory and others, that is a blinkered optimism worthy of Dr. Pangloss. They, by contrast, are deeply pessimistic about where this research will lead. Most of the RNA molecules that our cells make will probably not turn out to perform the sort of essential functions that hotair and firre do. Instead, they are nothing more than what happens when RNA-making proteins bump into junk DNA from time to time.

“You say, ‘I found it — America!’ ” says Alex Palazzo, a biochemist at the University of Toronto who co-wrote a spirited defense of junk DNA with Gregory last year in the journal PLOS Genetics. “But probably what you found is a little bit of noise.”

Palazzo and his colleagues also roll their eyes at the triumphant declarations being made about recent large-scale surveys of the human genome. One news release from an N.I.H. project declared, “Much of what has been called ‘junk DNA’ in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes.” Researchers like Gregory consider this sort of rhetoric to be leaping far beyond the actual evidence. Gregory likens the search for useful pieces of noncoding DNA to using a metal detector to find gold buried at the beach. “The idea of combing the beach is a great idea,” he says. But you have to make sure your metal detector doesn’t go off when it responds to any metal. “You’re going to find bottle caps and nails,” Gregory says.

He expects that as we examine the genome more closely, we’ll find many bottle caps and nails. It’s a prediction based, he and others argue, on the deep evolutionary history of our genome. Over millions of years, essential genes haven’t changed very much, while junk DNA has picked up many harmless mutations. Scientists at the University of Oxford have measured evolutionary change over the past 100 million years at every spot in the human genome. “I can today say, hand on my heart, that 8 percent, plus or minus 1 percent, is what I would consider functional,” Chris Ponting, an author of the study, says. And the other 92 percent? “It doesn’t seem to matter that much,” he says.

It’s no coincidence, researchers like Gregory argue, that bona fide creationists have used recent changes in the thinking about junk DNA to try to turn back the clock to the days before Darwin. (The recent studies on noncoding DNA “clearly demonstrate we are ‘fearfully and wonderfully made’ by our Creator God,” .) In a sense, this debate stretches back to Darwin himself, whose 1859 book, “On the Origin of Species,” set the course for our understanding natural selection as a natural “designer.” Later in his life, Darwin took pains to stress that there was more to evolution than natural selection. He was frustrated to see how many of his readers thought he was arguing that natural selection was the only force behind life’s diversity. “Great is the power of steady misrepresentation,” Darwin grumbled when he updated the book for its sixth edition in 1872. In fact, he wrote, he was quite open-minded about other forces that might drive evolution, like “variations that seem to us in our ignorance to arise spontaneously.”

Darwin was certainly ignorant about genomes, as scientists would continue to be for decades after his death. But Gregory argues that genomes embody the very mix of adaptation and arbitrariness that Darwin had in mind. Over millions of years, the human genome has spontaneously gotten bigger, swelling with useless copies of genes and new transposable elements. Our ancestors tolerated all that extra baggage because it wasn’t actually all that heavy. It didn’t make them inordinately sick. Copying all that extra DNA didn’t require them to draw off energy required for other tasks. They couldn’t add an infinite amount of junk to the genome, but they could accept an awful lot. To subtract junk, meanwhile, would require swarms of proteins to chop out every single dead gene or transposable element — without chopping out an essential gene. A genome evolving away its junk would lose the race to sloppier genomes, which left more resources for fighting diseases or having children.

The blood-drenched slides that pack Gregory’s lab with their giant genomes only make sense, he argues, if we give up thinking about life as always evolving to perfection. To him, junk DNA isn’t a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph.

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In Vietnam, Rampant Wildlife Smuggling Prompts Little Concern

U MINH, Vietnam — Luc Van Ho slips through a tangled thicket of jungle, graceful as a dancer. A blanket of dried bamboo and melaleuca leaves on the forest floor barely crackles beneath his bare feet. Only the smell of cigarette smoke betrays his presence.

A hunter, Mr. Luc, 45, set out at dawn from his family’s bamboo-thatched home in Vietnam’s U Minh forest to check a half dozen homemade traps rigged along animal trails in the underbrush and on canal banks frequented by snakes and turtles.

He stops at a snare trap made of wood and bicycle brake wire, nearly invisible beneath leaves. The trap is empty, not unusual.

“Before, this forest was very different,” Mr. Luc said. “Now, the animals are so few that most hunters are changing their jobs.”

Still, in the previous two weeks, Mr. Luc had caught nine Southeast Asian box turtles and Malayan snail-eating turtles, five elephant trunk snakes, a handful of water birds and two rare Himalayan griffon vultures. For safekeeping, Mr. Luc stashed the vultures in his brother’s house, leaving them tethered in the bedroom until he can figure out what to do with them.

In the past, Mr. Luc’s hunting trips often yielded wildlife bonanzas, including prized pangolins. Also known as scaly anteaters, they are among the most trafficked mammals in the world. .

Although he caught just two pangolins last year, that price makes it well worth the effort to keep seeking them out. He knows, however, that this lucrative resource is finite.

“Pangolins will be extinct soon,” he said. Still, he expresses no plans to retire.

Mr. Luc is one of thousands of illegal hunters draining Vietnam, one of the most biodiverse countries in the world, of its animals. Its rhinoceroses have already gone extinct, and conservationists estimate that just a couple of its tigers, if any, remain. Even lesser known species like soft-shell turtles and civets are sought out for traditional medicines, food, trophies and pets.

Illegal wildlife is one of the world’s largest contraband trades, netting an estimated $19 billion a year, not including illegal fisheries and timber. While all Southeast Asian countries and many others outside of the region are involved, Vietnam plays a paramount role. The country is a major thoroughfare for wildlife goods bound for China, which arrive overland from Cambodia, Thailand and Laos; by ship from Malaysia and Indonesia; or by air from Africa.

“After China, Vietnam is the next port of call in terms of where to look to figure out what’s going on with wildlife trade,” said Dan Challender, a co-chairman of the at the International Union for Conservation of Nature.

Vietnam is also a significant consumer of wildlife, especially those yielding the ingredients for traditional medicine, such as rhino horn, which is used to treat everything from cancer to hangovers. The exotic meats of rare animals are seen as luxuries by a rising middle class eager to advertise its prosperity.

“Pangolin is frequently the most expensive item on the menu, so ordering it is an obvious way to show off to friends and colleagues,” Dr. Challender said. “The fact that it’s illegal isn’t played down and is even attractive, because it adds this element that you live beyond the law.”

International concern about the trade has never been greater, but conferences, new enforcement strategies and ivory crushes have yet to make a dent.

In February, the Obama administration to curb illegal wildlife trade by strengthening enforcement, reducing demand and sending a handful of agents abroad. The United States is the second-largest market for illegal wildlife products, but only an estimated 10 percent of traffickers are caught because of inadequate resources supporting enforcement, as well as legal loopholes pertaining to certain products, such as ivory.

“Wildlife trade is higher profile now than it’s ever been, and that’s great,” said Chris Shepherd, regional director in Southeast Asia of , a wildlife trade monitoring network. “But all of the talk about this issue by world leaders is not trickling down to the ground yet.”

In January of this year, officials intercepted more than 7,500 protected pig-nosed turtles in Indonesia, a frozen tiger in Vietnam and 190 endangered black pond turtles in Singapore. As wildlife disappears in Southeast Asia, poachers increasingly turn to Africa.

More than 1,500 pounds of ivory and two tons of pangolin skins were intercepted in Uganda in January. Last year in South Africa alone, a record 1,215 rhinos were killed for their horns.

The illegal wildlife products that officials manage to interdict account for an estimated 10 to 20 percent of the total trafficked.

“We may be disrupting criminal networks, but we’re certainly not dismantling any of them,” said Scott Roberton, Vietnam country representative and regional coordinator for wildlife trafficking programs for the Wildlife Conservation Society. “The situation is going to get worse before it gets better.”

While China recently increased its arrests and prosecutions for wildlife crimes, those caught trafficking wildlife in Vietnam or other transit countries almost always escape punishment. Dealing in protected species is a criminal offense under Vietnamese law, as is selling wild-caught animals of any kind.

But even when trafficking kingpins are taken into custody, prosecution often depends on finding unrelated charges that are taken more seriously than wildlife crime, such as car smuggling. Poachers like Mr. Luc — who says he has never run into legal trouble — are rarely reprimanded, and punishment, if any, usually entails a small fine.

“Very few criminals caught for major violations like tiger or rhino horn possession ever do a day in prison,” said Douglas Hendrie, chief technical adviser for , a nonprofit organization based in Vietnam.

Wild-caught and protected animal products are easily procured in Vietnamese cities. “It’s not an enforcement priority yet, largely due to corruption, collusion and an absolute lack of concern,” Dr. Shepherd said. “People just do not care.”

Thien Vuong Tuu (“The Alcohol of the Gods”), a fancy restaurant in Ho Chi Minh City, advertises pangolin, bear, porcupine, bat and more on its illustrated menu. Customers interested in pangolin — sold for $150 a pound — must order it two to three hours in advance and place a deposit based on its weight.

When the customer returns for dinner, the manager presents the live pangolin to the table, then slices its throat on the spot to prove that the meat is fresh and has not been substituted.

“Pangolin is very popular with customers, because it treats a lot of sicknesses,” said Quoc Trung, the restaurant manager. His staff will also dry and package pangolin scales left over from dinner — a popular ingredient in traditional medicines that are still covered by Vietnamese health insurance.

On a Sunday night, families with young children and groups of middle-aged men fill the restaurant. At one table, two French-speaking men order a cobra to the delight of their female companions. Two young servers bring out a large, writhing snake, its mouth bound tightly shut with plastic twine.

As the customers film with their smartphones, one server holds the snake taut. The other carefully feels along the animal’s abdomen until he locates the heart, then opens it up with a pair of scissors and removes the beating organ with his bare fingers.

As the servers wring out the animal, the blood drips into a ceramic bowl to be mixed later with alcohol and drunk.

“The government doesn’t allow exotic meat, but we have our sources and good connections with the police,” Mr. Quoc said after the show concluded. “The demand is so high for these things, so we have to supply them.”

Given the widespread lack of enforcement, grass-roots conservation organizations in Vietnam increasingly find themselves on the front lines. Education for Nature-Vietnam recently conducted a survey of restaurants, hotels and shops in 12 districts in Hanoi and Ho Chi Minh City, recording each violation of wildlife laws and insisting that authorities follow up.

Several months later, the group repeated the survey and found the availability of illegal products ranging from snake “wine” to bear bile had fallen by nearly 60 percent in eight of the districts. “When authorities put us out of work by doing their job effectively and consistently, then we’ll no longer have to do this,” Mr. Hendrie said.

, a nonprofit based at Cuc Phuong National Park, organizes training sessions across the country for park rangers and the police, conducts community education programs and operates one of the country’s only rehabilitation centers for confiscated animals.

In Vietnam, much of the wildlife intercepted from illegal traders is sold by officials back into the black market. Nguyen Van Thain, Save Vietnam’s Wildlife’s founder, often must race to the sites of recent confiscations to try to recover animals before that can happen.

“Corrupt rangers still want to sell animals back to the trade,” Mr. Nguyen said. Even if the animals are not sold, very few return to the wild, because of a lack of rehabilitation facilities.

Animals not sent to a specialized rescue center often “just sit around until they die,” Dr. Shepherd said.

Over the last three months, Mr. Nguyen has helped rescue 20 pangolins, but the maximum capacity at his center — one of only two in Vietnam that can care for pangolins — is less than 50. With a budget of just $90,000 a year, he has few resources with which to expand the center and hire additional staff.

Mr. Nguyen says he is not confident that attitudes will change in time to spare his country’s wildlife.

“The problem in Vietnam is that conservation is a new way of thinking,” he said. “Vietnamese people need to learn to take seriously what we have now. We need to take care of our own environment and wildlife if we want it to be around in the future.”


A picture caption with an earlier version of this article misidentified a turtle captured by a poacher. It was a Malayan snail-eating turtle, not a Southeast Asian box turtle.

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Arizona Bill Would Ban Local Limits on Plastic Bags

PHOENIX — While other places have turned to bans and fees to discourage the use of plastic bags, Arizona is headed in a different direction.

On Thursday, the State Legislature here sent a bill to the governor that would ban the bans, with supporters seeing it as a way to protect businesses and consumers from a potential hodgepodge of regulations.

The bill would prevent cities and counties from regulating the “sale, use or disposition of auxiliary containers,” which include single-use disposable bags, boxes, cans and bottles. It would also prohibit requirements for businesses to report energy use.

State Senator Nancy Barto, the bill’s sponsor and a Republican, said that “excessive regulation on containers creates more work and cost for retailers and other businesses — and leads to higher consumer cost and a drag on economic growth.”  She added: “Municipalities acting on their own to implement these mandates run counter to the state’s goal to overcome Arizona’s sluggish job growth and economic stability.”

The only city to carry out any such rule is Bisbee, southeast of Tucson, which banned single-use plastic bags and requires a 5-cent charge per paper bag.

Lauren Kuby, a city councilwoman in Tempe, cited estimates that 50 million single-use plastic bags are used each year in the city and that less than 5 percent are recycled. She said the city faced costs from litter, as well as from the damage the plastic bags caused to machinery at recycling facilities.

In a state where leaders often rebel against federal oversight, Ms. Kuby accused legislators of taking away the decision-making authority of local officials. “It’s a very ironic thing, and it’s poor public policy,” she said.

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A Map Of Lightning Strikes Around the World

Lightning Map

Lightning Map

Lightning strikes are one of those dangerous natural occurrences that happen all over the world, spawning and adding a bit of atmospheric flair to movies and ghost stories.

But there are definitely some places where lightning strikes more often than others. The map above was created using nearly 20 years of data from two satellites, which recorded lightning flashes from 1995 to 2013. The map looks at the average number of strikes per square kilometer. Areas with low amounts of lightning are colored purple and areas with higher amounts are in pink.

The countries with the are Venezuela and the Democratic Republic of the Congo. If you want to avoid lightning, try going somewhere in the middle of an ocean towards either one of the poles. Because lightning tends to strike on land and closer to the equator, you'll have a better chance of eluding the strikes (though you might get cold ... or seasick).

Lightning tends to occur mostly on land near the equator because that's where the heat is. Lightning-generating storms in areas where there is a large difference in temperature between lower levels of the atmosphere and layers further up. Land heats up more quickly than the ocean (just think about the difference between a swimming pool and the sidewalk on a hot day) and areas near the equator get more sun than the poles.

The researchers who put together this map are part of a NASA-affiliated group called the which sounds like a rapid-response superhero group. Their next mission is to put more lightning sensors in space, on the ISS and in geostationary orbit, to monitor storms around the world.

[Via ]
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Behind Each Breath, an Underappreciated Muscle

Some muscles get all the glory. Bodybuilders show off their swollen triceps; sprinters flash their sharp-edged calves. But deep inside all of us, a sheet of muscle does heroic work in obscurity.

In order to breathe in, we must flatten the dome-shaped diaphragm; to breath out, we let it relax again. The diaphragm delivers oxygen to us a dozen times or more each minute, a half-billion times during an eighty-year life.

“We are completely dependent on the diaphragm,” said , a biologist at the University of Utah. “But we take it for granted every moment we’re breathing.”

To Dr. Kardon, the diaphragm is not just underappreciated but puzzling. All mammals, from platypuses to elephants, have a diaphragm. But no other animal has one. “We have a very different solution for breathing than reptiles and birds,” said Dr. Kardon.

Before the evolution of a diaphragm, our reptilelike ancestors probably breathed the way many reptiles do today. They used a jacket of muscles to squeeze the rib cage.

Once the diaphragm evolved, breathing changed dramatically. Mammals gained a more powerful, efficient means to draw in a steady supply of oxygen. The evolution of a diaphragm may thus have made it possible for mammals to then evolve a warm-blooded metabolism. Without a diaphragm, humans might not have been able to evolve giant — but oxygen-hungry — brains.

Scientists suspect that the diaphragm evolved through some change in the way mammal embryos develop: Mutations caused certain embryonic cells to grow into an entirely new muscle. Dr. Kardon and other researchers are trying to understand that shift and why the muscle sometimes fails to develop, with catastrophic consequences.

One in every 2,500 babies is born with a hole in its diaphragm. The baby’s liver, intestines and other abdominal organs can push up through this opening against the lungs, stunting their growth and restricting the baby’s breathing. About a third of babies born with congenital diaphragmatic hernias die, and it is likely that still more die of this defect before birth.

Scientists have found that mutations in certain genes can increase the risk of developing hernias. But they have struggled to figure out exactly how these genes build the diaphragm. Dr. Kardon and her colleagues recently developed a set of new tools get a closer look. They last week in Nature Genetics.

They engineered mice so that certain types of cells would glow inside mouse embryos. Then they tracked the cells as they multiplied and migrated.

The diaphragm begins as a pair of folds flanking the esophagus, she and her colleagues found. These folds then expand in two waves. “It’s beautiful, aesthetically,” said Dr. Kardon.

In the first wave, one set of cells in the folds multiplies outward, toward the sides of the body. Then these cells fan out toward the front and back. The cells become connective tissue, forming a thin membrane across the top of the liver.

In the second wave, muscle-generating cells emerge from the folds. They follow the trail blazed by the connective tissue, forming a second sheet sandwiched inside the membrane. “The muscle cells are kind of dumb, and they’re just following the connective tissue,” said Dr. Kardon.

As part of their experiment, Dr. Kardon and her colleagues examined GATA4, a gene linked to diaphragmatic hernias. They engineered mouse embryos in which they could shut down GATA4 only in certain types of cells, and only at certain points in development.

In one trial, the scientists turned off GATA4 in the muscle cells in the diaphragm. In these cases, the mice formed diaphragms. But when the researchers shut down GATA4 in the connective tissue, the mice developed hernias.

Connective tissue cells must be using GATA4 to lay down a chemical trail for muscle cells, Dr. Kardon concluded. They can still lay down the trail if they have one defective copy of the GATA4 gene.

Each time the connective tissue cells divide, there is a chance that a working copy of GATA4 may mutate, too. If that happens, the mutant cell and its descendants can’t lay down a trail, resulting in a gap in the sheet of muscle.

As the liver pushes against the diaphragm, the pressure creates intense stress in the gap, causing the diaphragm to rupture.

, a geneticist at Harvard Medical School, said that the new study offers a molecular explanation for how congenital diaphragmatic hernias occur. “I think it is a beautiful study and terribly important,” he said.

John J. Greer, a biologist at the University of Alberta, said he was skeptical that this scenario could account for most hernias.

He noted that most medical cases of congenital diaphragmatic hernias occur in the back left or right corners of the diaphragm. Dr. Kardon and her colleagues produced many hernias in the middle or front of the diaphragm of their mouse subjects.

Dr. Kardon countered that a lot of hernias occur in other parts of the diaphragm, but doctors fail to notice many of them. Since the lungs sit at the back of the diaphragm, hernias there can be dangerous. Hernias elsewhere can be harmless.

“Because they don’t have serious medical consequences, they go unnoticed,” she said.

It is possible that the diaphragm may have evolved in two waves, much as it develops in the embryo. Dr. Kardon suggested that the ancestors of mammals may have evolved a connective tissue sheet first, simply to separate the lungs from the abdomen.

Only later did muscles form a sandwiched layer, creating a breathing pump.

This transition may not have required a lot of mutations. Muscle cells follow chemical trails made by connective tissue in other parts of the body. Once the connective tissue cells started making a proto-diaphragm, muscle cells already had the molecular machinery required to follow them.

“The mechanism is already in place,” said Dr. Kardon. “It’s a relatively simple step, even if it sounds like an impossible chasm.”

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