Nearly Two-Thirds of Cancers Are Due to Random DNA ‘Mistakes’

Posted but not written by Lou Sheehan

Nearly Two-Thirds of Cancers Are Due to Random DNA ‘Mistakes’

Nearly Two-Thirds of Cancers Are Due to Random DNA 'Mistakes'

Credit: Cell division via Shutterstock

Cancer is caused by mistakes in DNA, and a new study finds that in most cancer cases, these mistakes are completely random; they’re not due to heredity or environmental factors, but rather the result of random errors.

The mistakes, or mutations, cause cancer to happen because even a tiny error in DNA can make cells multiply out of control, the study said. Scientists had thought these mutations resulted mainly from two things: Either the mutation was inherited, or it was caused by outside factors that can damage DNA, such as cigarette smoke or ultraviolet radiation, the researchers wrote.

But a third cause — random mistakes — actually accounts for two-thirds of these mutations, said the new study, published today (March 23) in the journal Science.

When a cell divides, it copies its DNA, so that each of the new cells will have its own version of the genetic material. But each time this copying happens, it creates an opportunity for a mistake to occur. And in some cases, these mistakes can lead to cancer. [10 Do’s and Don’ts to Reduce Your Risk of Cancer]

This means that cancer “will occur no matter how perfect the environment,” senior study author Dr. Bert Vogelstein, a pathologist at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, said in a statement.

In the new study, the researchers wanted to calculate what percentage of cancers were due to heredity, the environment and random mistakes. The scientists developed a mathematical model that incorporated data from registries of cancer patients around the world and data from DNA sequencing.

About 66 percent of cancers were due to random mistakes, 29 percent of cancers were due to environmental factors or people’s lifestyles, and 5 percent of cancers were due to inherited mutations, the study found. This result, the researchers noted, lined up somewhat with an estimate from Cancer Research UK that 42 percent of cancers could be prevented with changes to lifestyle.

Some types of cancer, such as brain and prostate cancer, are nearly entirely attributable to random mistakes, the study said. The researchers found that random mistakes had caused more than 95 percent of these cancer cases that were looked at in the study.

For some other cancers, however, environmental factors play a large role, the study found. For example, environmental factors, primarily smoking, caused 65 percent of all lung cancers in the study, the researchers found. Just 35 percent of lung cancers were due to random mistakes, the investigators found.

In this image, the researchers used red coloring to indicate the percentage of cancers that are attributed to inherited mutations (left), random mistakes (center) and environmental factors (right) in women. For each organ, the color represents what percentage is attributable to each factor, ranging from white (0 percent) to red (100 percent). <br></br>The cancers are identified as: B, brain; Bl, bladder; Br, breast; C, cervical; CR, colorectal; E, esophagus; HN, head and neck; K, kidney; Li, liver; Lk, leukemia; Lu, lung; M, melanoma; NHL, non-Hodgkin lymphoma; O, ovarian; P, pancreas; S, stomach; Th, thyroid; U, uterus.

In this image, the researchers used red coloring to indicate the percentage of cancers that are attributed to inherited mutations (left), random mistakes (center) and environmental factors (right) in women. For each organ, the color represents what percentage is attributable to each factor, ranging from white (0 percent) to red (100 percent).

The cancers are identified as: B, brain; Bl, bladder; Br, breast; C, cervical; CR, colorectal; E, esophagus; HN, head and neck; K, kidney; Li, liver; Lk, leukemia; Lu, lung; M, melanoma; NHL, non-Hodgkin lymphoma; O, ovarian; P, pancreas; S, stomach; Th, thyroid; U, uterus.

Credit: C. Tomasetti et al,. Science (2017)

In this image, the researchers used red coloring to indicate the percentage of cancers that are attributed to inherited mutations (left), random mistakes (center) and environmental factors (right) in women. For each organ, the color represents what percentage is attributable to each factor, ranging from white (0 percent) to red (100 percent).

The cancers are identified as: B, brain; Bl, bladder; Br, breast; C, cervical; CR, colorectal; E, esophagus; HN, head and neck; K, kidney; Li, liver; Lk, leukemia; Lu, lung; M, melanoma; NHL, non-Hodgkin lymphoma; O, ovarian; P, pancreas; S, stomach; Th, thyroid; U, uterus.
Credit: C. Tomasetti et al,. Science (2017)

A single mutation in a cell is unlikely to cause cancer, Vogelstein noted, speaking in a podcast produced by Johns Hopkins. Rather, the more mutations there are, the more likely it is that the cell will turn cancerous, he said.

Thus, mutations from random mistakes are enough to cause cancer by themselves in some cases, Vogelstein said. But in others, a combination of random mistakes, plus mistakes due to environmental factors eventually turns the cell cancerous, he said. For example, skin cells have a baseline level of mutations due to random mistakes, and exposure to ultraviolet light can add even more mutations, leading to cancer, he said. [How to Protect Yourself from Sun and Heat in 2017]

Cristian Tomasetti, an assistant professor of biostatistics also at Johns Hopkins, likened the three causes of mutations to typos that occur while using a keyboard. Some of those typos may be the result of the typist being tired or distracted; these can be thought of as the environmental factors, Tomasetti said on the podcast. And if the keyboard the typist is using is missing a key, that’s a hereditary factor, Tomasetti said.

But even in a perfect environment, where the typist is perfectly rested and using a perfectly working keyboard, typos will still occur, Tomasetti said. And these represent the random mistakes.

There are prevention strategies for cancers caused by environmental factors or inherited genes: A smoker can quit smoking to help lower his or her risk of lung cancer, and a woman who finds that she carries the breast cancer BRCA mutation may opt to have a preventative mastectomy.

These “primary prevention” strategies are considered the best way to reduce deaths from cancers, the researchers wrote in the study.

Such primary prevention is not possible for cancers caused by random mutations, but still, “secondary prevention” can help save lives, the authors wrote. Secondary prevention refers to early detection of cancer, according to the study.

“We need to focus more on early detection, because these are not mutations” that can be avoided, Tomasetti said on the podcast.

Originally published on Live Science.

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Special Report : Aircraft carriers, championed by Trump, are vulnerable to attack

By Scot Paltrow | WASHINGTON

Last week, President Donald J. Trump chose the deck of the newest U.S. aircraft carrier, the $13 billion USS Gerald R. Ford, for a speech extolling his planned boost in military spending.

Trump vowed that the newest generation of “Ford Class” carriers – the most expensive warships ever built – will remain the centerpiece of projecting American power abroad.

“We’re going to soon have more coming,” Trump told an enthusiastic audience of sailors, declaring the new carriers so big and solidly built that they were immune to attack.

Trump vowed to expand the number of carriers the United States fields from 10 to 12. And he promised to bring down the cost of building three “super-carriers,” which has ballooned by a third over the last decade from $27 to $36 billion.

The Gerald R. Ford alone is $2.5 billion over budget and three years behind schedule, military officials say. The second Ford-class carrier, the John F. Kennedy, is running five years late.

Trump’s expansion plans come as evidence mounts that potential enemies have built new anti-ship weapons able to destroy much of the United States’ expensive fleet of carriers. And as they have been for decades, carriers remain vulnerable to submarines.

In a combat exercise off the coast of Florida in 2015, a small French nuclear submarine, the Saphir, snuck through multiple rings of defenses and “sank” the U.S. aircraft carrier Theodore Roosevelt and half of its escort ships. In other naval exercises, even old-fashioned diesel-electric submarines have beaten carriers.

All told, since the early 1980s, U.S. and British carriers have been sunk at least 14 times in so-called “free play” war games meant to simulate real battle, according to think tanks, foreign navies and press accounts. The exact total is unknown because the Navy classifies exercise reports.

Today, the United States is the only country to base its naval strategy on aircraft carriers. The U.S. fleet of 10 active carriers is 10 times as big as those deployed by its primary military rivals, Russia and China, who field one active carrier each.

Roger Thompson, a defense analyst and professor at Kyung Hee University in South Korea, says the array of powerful anti-ship weapons developed in recent years by potential U.S. enemies, including China, Russia and Iran, increase carriers’ vulnerability.

The new weapons include land-based ballistic missiles, such as China’s Dong Feng-21 anti-ship missile, which has a claimed range of 1,100 miles (1,770 kilometers) and moves at 10 times the speed of sound. Certain Russian and Chinese submarines can fire salvoes of precision-guided cruise missiles from afar, potentially overwhelming carrier-fleet anti-missile defense.

Russia, China, Iran and other countries also have so-called super-cavitating torpedoes. These form an air bubble in front of them, enabling them to travel at hundreds of miles per hour. The torpedoes cannot be guided, but if aimed straight at a ship they are difficult to avoid.

A 2015 Rand Corporation report, “Chinese Threats to U.S. Surface Ships,” found that if hostilities broke out, “the risks to U.S. carriers are substantial and rising.”

“Beyond a shadow of a doubt, a carrier is just a target,” says defense analyst Pierre Sprey, who worked for the U.S. Secretary of Defense’s office from 1966 to 1986 and is a longtime critic of U.S. weapons procurement.

 

DEFENDING CARRIERS

Navy leaders stand by the carrier. In an interview late last year, Admiral Scott Swift, commander of the U.S. Pacific Fleet, lauded carriers’ versatility. Swift says they remain “very viable,” sufficiently impregnable to be sent into the thick of combat zones.

Swift said he would order carriers into close battle “in a heartbeat.” Nevertheless, citing the new anti-ship weapons, Swift says the carrier “is not as viable as it was 15 years ago.”

Trump has said he will make good on his campaign promise to increase the Navy’s fleet to 350 ships. The Navy currently has 277 deployable ships. The cost of a single new, Ford-class carrier – $10.5 billion without cost overruns – would consume nearly 20 percent of Trump’s proposed $54 billion increase in next year’s defense budget.

Some critics, including former senior Defense Department personnel, say Washington has put too much of the country’s defense budget into a handful of expensive, vulnerable carriers.

At a naval symposium in 2010, then-Secretary of Defense Robert Gates called into question making such big investments in a few increasingly sinkable ships. Gates said “a Ford-class carrier plus its full complement of the latest aircraft would represent potentially $15 billion to $20 billion worth of hardware at risk.”

The Navy, with the backing of Congress, went ahead nevertheless. The program has strong Congressional backing. In the 1990s, when defense spending was cut after the end of the Cold War, Congress enacted a law requiring the Navy to maintain an 11-carrier fleet.

Congress has given the Navy a temporary exemption to have 10 active carriers while one is overhauled. When the Ford is commissioned, it will bring the U.S. carrier fleet to 11.

Trump did not specify in his speech how he would bring the carrier fleet to 12. But he said the Ford-class carriers would be invulnerable to attack because they represent the best in American know-how.

“There is no competition to this ship,” declared Trump, who called the Gerald R. Ford American craftsmanship “at its biggest, at its best, at its finest.”

 

FAILING SYSTEMS

Trump did not mention that the ship’s builder, Huntington Ingalls Industries, launched the Ford more than three years ago, but the Navy has yet to commission it and put it into service because of severe flaws. Many of its new high tech systems failed to work, including such basic ones as the “arresting gear” that catches and stops landing jets.

The Navy says the ship will be commissioned sometime this year. But the criticism has continued.

In a written statement in July, John McCain, chairman of the Senate Armed Services Committee, noted the cost overruns and cited a list of crucial malfunctioning systems that remained unfixed. “The Ford-class program is a case study in why our acquisition system must be reformed,” McCain wrote.

Ray Mabus, who in January stepped down as secretary of the Navy, said in an interview that the Gerald R. Ford “is a poster child for how not to build a ship.” He added: “Everything that could have been done wrong was done wrong.”

Mabus said that because of commitments made before he became Navy secretary, the Ford was loaded with high-tech equipment that had not even been designed yet. He also faulted awarding the shipbuilder a “cost plus” contract, under which it gets a fixed profit regardless of how much it costs to build the vessel. “There was no incentive to hold down costs,” Mabus said.

Others criticize carriers as strategically flawed. Jerry Hendrix, a retired Navy captain and Defense Department official, is now director of the Defense Strategies and Assessments Program at the Center for a New American Security. Carriers, he said in an email exchange, give Washington’s rivals a cheap opportunity to score big. For the cost of a single carrier, he calculates, a rival can deploy 1,227 anti-carrier missiles.

“The enemy can build a lot more missiles than we can carriers for equivalent investments,” Hendrix said, “and hence overwhelm our defensive capabilities.”

The most commonly proposed alternative to carriers is building a much larger number of smaller, nimbler vessels, including submarines and surface ships. Submarines don’t require escorts and can hit distant targets on land. And carriers have not been tested in battle against an enemy able to fight back since World War II – more than 70 years ago.

The Navy and some outside defense experts say that despite increased threats, carriers remain fully viable and perform an essential service. They laud carriers’ mobility and swiftness, enabling the United States to project air power to places otherwise unreachable.

Carrier proponent Bryan McGrath, the deputy director of the Hudson Institute’s Center for American Seapower in Washington, said carriers are less vulnerable than stationary, land-based air bases.

“A carrier is a big floating airport, and not only a floating airport, but it moves at 40 knots,” says McGrath, a former captain of a guided missile destroyer. “How much more vulnerable are airfields on land that don’t move?”

But Sprey, the former Defense Department official and longtime Pentagon procurement critic, says carriers waste funds that could be used to build more cost-effective weapons systems.

“Every Ford-class carrier we build detracts from U.S. defense,” Sprey said.

 

LIMITED PROTECTION

Both strong supporters of carriers as well as opponents agreed that there is a serious flaw in the current configuration of U.S. carriers: their complement of strike aircraft. Almost all are short-range jets, the F-18 Hornet, whose range could render the planes useless in some conflicts.

The Chinese, in particular, have established sea zones bristling with anti-ship weapons meant to make it impossible for enemy flotillas to enter.

Top U.S Navy commanders, including Pacific commander Swift and Vice Admiral Mike Shoemaker, the Navy “Air Boss” in charge of carriers, say carriers could safely enter such zones long enough to carry out a mission. But many outside analysts say a U.S. president would be hesitant to risk such an expensive ship and the lives of up to 5,500 crew members.

In order to be relatively safe, a carrier would have to stand off by 1,300 nautical miles, or 2,300 kilometers – out of range of the Dong Feng missiles. And the F-18s have a range of only 400 nautical miles (equal to 460 statute miles or 740 kilometers) to a target with enough fuel to return.

Experts on both sides of the debate say that if the carriers have to stand off, the Hornets would have to be refueled in midair an impractical number of times while flying to and from their targets. It thus would be all but impossible for carriers to send air power into war zones.

The F-18s are to be replaced by 2020 with new F-35C Lightning IIs, but these have only a marginally better range of 650 nautical miles.

The Hudson Institute’s McGrath, who champions carriers, says the short-range jets impair the mission.

“What they (the Navy) haven’t done yet is to design and fund a strike aircraft that can fly 1,000 miles, drop its bombs and come home,” McGrath said.

The cost of carriers in terms of strategy and money is multiplied because carriers do not travel alone. For protection, they move with large escorts, making every “carrier strike group” a virtual armada.

Each carrier usually has an escort of at least five warships, a mixture of destroyers and cruisers, at least one submarine and a combined ammunition-supply ship and helicopters designed to detect subs. When close enough to shore, carriers are also protected by new, land-based P-8 Poseidon jets, designed to detect and destroy subs.

 

OLD THREATS

For carrier commanders, the most feared weapon is a 150-year-old one. A single, submarine-launched torpedo could send a carrier to the bottom.

Most modern torpedoes aren’t targeted to hit ships. Instead they are programmed to explode underneath. This creates an air bubble that lifts the ship into the air and drops it, breaking the hull.

For decades, critics have faulted the Navy for failing to develop effective defenses against modern torpedoes. A 2016 report by the Pentagon’s Office of Operational Test and Evaluation said the Navy has recently made significant progress, but the systems still have crucial deficiencies.

Experts also say that carriers are at risk from updated versions of one of the oldest naval vessels still in use: the diesel-electric submarine. These were the subs used in both World Wars.

Diesel-electric subs have the advantage of being small – and while on electric power, silent, and in general quieter and harder to detect than nuclear subs.

Diesel-electric subs are also far cheaper to build than nuclear ones. Allies and rivals have been building large numbers of them. Worldwide, more than 230 diesel-electric subs are in use. China has 83 in use, while Russia has 19.

Hendrix, the former Defense Department official, says the carriers’ vulnerabilities make the fleet a profligate use of money, vessels and aircraft.

“We have paid billions of dollars to build ships that are largely defensive in their orientation, thus taking away from the offensive power of the fleet,” Hendrix says. “In the end, we spend a lot of money on defense to send 44 strike aircraft off the front end of a carrier.”

 

(Editing by David Rohde. Reporting by Scot Paltrow.)

 

http://www.reuters.com/article/us-usa-trump-carriers-specialreport-idUSKBN16G1CZ?utm_source=Sailthru&utm_medium=email&utm_campaign=US%20Reuters%20News%20Now%202017-03-09&utm_term=US%20Reuters%20News%20Now

Posted, but not writtn, by Lou Sheehan.

 

 

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World’s Oldest Fossils Possibly Uncovered in Canada

Posted but not written by Louis Sheehan

World’s Oldest Fossils Possibly Uncovered in Canada

World's Oldest Fossils Possibly Uncovered in Canada

Scientists recently found evidence of ancient lifeforms in rocks in Canada. Within these fossils were tiny tubes of a mineral called hematite, a form of iron. The researchers believe these tubes are relics of an ancient form of microbial life that lived near hydrothermal vents.

Credit: Matthew Dodd

Ancient traces of microbial life that are between 3.77 billion and 4.29 billion years old might have been unearthed in a rocky outcropping in Canada, a new study suggests. However, some scientists are casting doubt on what the findings truly mean.

If the new microfossils truly are evidence of primordial life that once sprang up in ancient hydrothermal vents, it suggests that life began on Earth soon after the planet coalesced, the study authors said.

“We can say life managed to emerge on Earth very rapidly almost soon after the oceans had condensed on the surface of the Earth 4.4 billion years ago,” said study lead author Matthew Dodd, a biogeochemistry graduate student at the University College London. “What this means is that life may not be such a difficult process to start once we have the right conditions and ingredients.”

However, not everyone is convinced: One scientist says there’s no way to say for sure that these traces are evidence of life — or that they are truly ancient. [In Images: The Oldest Fossils on Earth]

There’s no doubt that life has clung to our watery planet for much of its 4.5-billion-year history, but exactly when that life first emerged has been hotly debated. Scientists have found chemical signatures associated with life in 4.1-billion-year-old zircons from Australia. Filamentous structures threading through rocks in Australia were initially identified as 3.5-billion-year-old microbial mats. And fossils in Greenland contain traces of what might have been primeval cyanobacteria that first emerged 3.7 billion years ago.

The trouble is that it’s difficult for scientists to pin down signs of tiny life-forms that lived billions of years ago, when the Earth has gone through so many other changes since then.

For instance, the 3.5-billion-year-old rocks identified in Australia, known as the Apex Chert, were initially touted as tiny microfossils, but a subsequent analysis found that the chemical remains were tied to nonbiological processes from hydrothermal vents, said Kurt Konhauser, a geomicrobiologist at the University of Alberta who was not involved in the new study. Furthermore, the 3.7-billion-year-old fossils found in Greenland could have gotten their intriguing chemical signature from a nonbiological process, according to the new study, which was published today (March 1) in the journal Nature.

In the study, Dodd and his colleagues identified a rocky outcropping of primitive ocean crust in Quebec, Canada, made up mostly of volcanic lava rock. Sprinkled within this rock are ancient forms of zircon that are at least 3.7 billion years old — a finding that suggests the rock formation itself has ancient origins.

Inside some of the deeper portions of this rock, which likely have not been subjected to more recent effects, the researchers found tiny, wavy filaments and tube-like structures several times thinner than a hair.

“You’re not going to see these without a microscope,” Dodd told Live Science.

These structures resemble later microbial fossils that have been unearthed in Lokken, Norway, and California. These later fossils, which come from hydrothermal vents, are just 180 million and 450 million years old, respectively.

The team also found chemical signatures associated with life, such as higher ratios of lighter versus heavier isotopes (or versions) of carbon. [Video: Ancient Signs of Life Found in Canadian Rocks]

“Life prefers to use the lighter isotopes to build its molecules,” Dodd said.

In addition, the team found distinctive “rosettes” of carbonate, along with a chemical called apatite interwoven through them. Apatite forms when phosphorus, an element needed by all life-forms, decays and combines with other rocks in the environment.

Tiny granules that might have formed when these organic life-forms decayed and reacted with seafloor minerals also point to life, as similar granules are found around more modern fossils, such as those of ammonites, Dodd said.

Finally, the team found forms of iron in the rocks that could have been formed by iron-oxidizing, hydrothermal vent bacteria, the researchers reported. The team also ruled out several alternative explanations, such as the wavy structures forming through rock stretching.

The researchers have provided a lot of solid evidence to support their claim for ancient life, Konhauser said.

“They’ve gone a lot further than most other papers ever have; but it’s not conclusive, and it never will be,” Konhauser told Live Science.

The problem is that it’s incredibly tricky to show both that the formations are proof of life, and that those traces of life are truly as old as the researchers say they are.

“These rocks are crosscut by lots of different hydrothermal vanes; over 4 billion years, lots of fluids have moved through these rocks,” Konhauser said. As such, it’s possible to argue that the signs of life may be more recent, even if the rocks themselves are ancient, he added.

The other issue is that the team is arguing that ancient life-forms were oxidizing iron at least 3.8 billion years ago, far below the water’s surface, near hydrothermal vents, he said. For microbes to oxidize iron, oxygen must reach lower ocean depths. But most scientists think the deep ocean didn’t get oxygen so early on.

In modern times, oxygen reaches the deep ocean in part because cold water from the icy poles forms down-welling currents that carry oxygen deeper, Konhauser said. No one knows whether there were poles at that time and, if there were, how oxygen would have reached the deep ocean, he added. (There are cyanobacteria that can oxidize iron while lying in shallow waters using sunlight, but the new study is claiming that the bacteria came from hydrothermal vents, Konhauser said.)

So, although multiple individual lines of evidence do point to the structures being evidence of life, the problem occurs when they try to weave those pieces of evidence into a complex story, Konhauser said.

“Just because it looks like something, doesn’t mean it is,” he said.

Originally published on Live Science.

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Hannah Arendt, The Origins of Totalitarianism

“The ideal subject of totalitarian rule is not the convinced Nazi or the dedicated communist, but people for whom the distinction between fact and fiction, true and false, no longer exists.”
― Hannah ArendtThe Origins of Totalitarianism
“One of the greatest advantages of the totalitarian elites of the twenties and thirties was to turn any statement of fact into a question of motive.”
― Hannah ArendtThe Origins of Totalitarianism
“Before mass leaders seize the power to fit reality to their lies, their propaganda is marked by its extreme contempt for facts as such, for in their opinion fact depends entirely on the power of man who can fabricate it.”
― Hannah ArendtThe Origins of Totalitarianism
“In an ever-changing, incomprehensible world the masses had reached the point where they would, at the same time, believe everything and nothing, think that everything was possible and that nothing was true. … Mass propaganda discovered that its audience was ready at all times to believe the worst, no matter how absurd, and did not particularly object to being deceived because it held every statement to be a lie anyhow. The totalitarian mass leaders based their propaganda on the correct psychological assumption that, under such conditions, one could make people believe the most fantastic statements one day, and trust that if the next day they were given irrefutable proof of their falsehood, they would take refuge in cynicism; instead of deserting the leaders who had lied to them, they would protest that they had known all along that the statement was a lie and would admire the leaders for their superior tactical cleverness.”
― Hannah ArendtThe Origins of Totalitarianism
Posted by Lou Sheehan
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The Universe is Flat Neta Bahcall (Princeton)

See, for example, the discussion on pages 1485 and 1486 (as well as the rest of the article) ….

— Louis Sheehan
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Ganzfeld Effect Notes

On episode 268 of Howard Hughes’ “The Unexplained he interviewed Dr. Caroline Watt of Edinburgh University.  At about minute 13:30 (and again at 24:35) on my itunes version of the show.

she refers briefly to the ganzfeld effect.  It seems to have some different wrinkles in her hands. You might care to try to book her?
It isn’t a particular interest of mine, but I mention it in another wild stab at trying to be helpful.
Wikipedia on Caroline Watt: https://en.wikipedia.org/wiki/Caroline_Watt
posted by Louis Sheehan
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Questions Cloud Risky Raid That Killed an American Commando in Yemen By ERIC SCHMITT and DAVID E. SANGER FEB. 1, 2017

 

 

Posted but not written by Louis Sheehan

 

Photo

Officials, including Senator Chris Coons of Delaware, left Washington for Dover Air Force Base on Wednesday to meet the family of an American commando killed in Yemen. CreditStephen Crowley/The New York Times

WASHINGTON — Just five days after taking office, over dinner with his newly installed secretary of defense and the chairman of the Joint Chiefs of Staff, President Trump was presented with the first of what will be many life-or-death decisions: whether to approve a commando raid that risked the lives of American Special Operations Forces and foreign civilians alike.

President Barack Obama’s national security aides had reviewed the plans for a risky attack on a small, heavily guarded brick home of a senior Qaeda collaborator in a mountainous village in a remote part of central Yemen. But Mr. Obama did not act because the Pentagon wanted to launch the attack on a moonless night and the next one would come after his term had ended.

With two of his closest advisers, Jared Kushner and Stephen K. Bannon, joining the dinner at the White House along with Defense Secretary Jim Mattis and Gen. Joseph F. Dunford Jr., Mr. Trump approved sending in the Navy’s SEAL Team 6, hoping the raid early last Sunday would scoop up cellphones and laptop computers that could yield valuable clues about one of the world’s most dangerous terrorist groups. Vice President Mike Pence and Michael T. Flynn, the national security adviser, also attended the dinner.

As it turned out, almost everything that could go wrong did. And on Wednesday, Mr. Trump flew to Dover Air Force Base in Delaware to be present as the body of the American commando killed in the raid was returned home, the first military death on the new commander in chief’s watch.

The death of Chief Petty Officer William Owens came after a chain of mishaps and misjudgments that plunged the elite commandos into a ferocious 50-minute firefight that also left three troops wounded and a $75 million aircraft deliberately destroyed. There are allegations — which the Pentagon acknowledged on Wednesday night are most likely correct — that the mission also killed several civilians, including some children. The dead include, by the account of Al Qaeda’s branch in Yemen, the 8-year-old daughter of Anwar al-Awlaki, the American-born Qaeda leader who was killed in a targeted drone strike in 2011.

Mr. Trump on Sunday hailed his first counterterrorism operation as a success, claiming the commandos captured “important intelligence that will assist the U.S. in preventing terrorism against its citizens and people around the world.” A statement by the military’s Central Command on Wednesday night that acknowledged the likelihood of civilian casualties also said the captured materials had provided some initial information helpful to counterterrorism analysts. The statement did not provide details.

But the mission’s casualties raise doubts about the months of detailed planning that went into the operation during the Obama administration and whether the right questions were raised before its approval. Typically, the president’s advisers lay out the risks, but Pentagon officials declined to characterize any discussions with Mr. Trump.

A senior administration official said on Wednesday night that the Defense Department had conducted a legal review of the operation that Mr. Trump approved and that a Pentagon lawyer had signed off on it.

Mr. Trump’s new national security team, led by Mr. Flynn, the former head of the Defense Intelligence Agency and a retired general with experience in counterterrorism raids, has said that it wants to speed the decision-making when it comes to such strikes, delegating more power to lower-level officials so that the military may respond more quickly. Indeed, the Pentagon is drafting such plans to accelerate activities against the Qaeda branch in Yemen.

But doing that also raises the possibility of error. “You can mitigate risk in missions like this, but you can’t mitigate risk down to zero,” said William Wechsler, a former top counterterrorism official at the Pentagon.

In this case, the assault force of several dozen commandos, which also included elite troops from the United Arab Emirates, was jinxed from the start. Qaeda fighters were somehow tipped off to the troops’ stealthy advance toward the village — perhaps by the whine of American drones that local tribal leaders said were flying lower and louder than usual.

With the crucial element of surprise lost, the Americans and Emiratis found themselves in a gun battle with Qaeda fighters who took up positions in other houses, a clinic, a school and a mosque, often using women and children as cover, American military officials said in interviews this week.

The commandos were taken aback when some of the women grabbed weapons and started firing, multiplying the militant firepower beyond what the troops had expected. The Americans called in airstrikes from helicopter gunships and fighter aircraft that helped kill some 14 Qaeda fighters, but not before an MV-22 Osprey aircraft involved in the operation experienced a “hard landing,” injuring three more American personnel on board. The Osprey, which the Marine Corps said cost $75 million, was badly damaged and had to be destroyed.

The raid, some details of which were first reported by The Washington Post, also destroyed much of the village of Yakla, and left senior Yemeni government officials seething. Yemen’s foreign minister, Abdul Malik Al Mekhlafi, condemned the raid on Monday in a post on his official Twitter account as “extrajudicial killings.”

Baraa Shiban, a Yemeni fellow for Reprieve, a London-based human rights group, said he spoke by phone to a tribal sheikh in the village, Jabbr Abu Soraima, who told him: “People were afraid to leave their houses because the sound of choppers and drones were all over the sky. Everyone feared of being hit by the drones or shot by the soldiers on the ground.”

After initially denying there were any civilian casualties, Pentagon officials backtracked somewhat on Sunday after reports from the Yemeni authorities begin trickling in and grisly photographs of bloody children purportedly killed in the attack appeared on social media sites affiliated with Al Qaeda’s branch in Yemen.

Capt. Jeff Davis, a Pentagon spokesman, said on Monday that some of the women were combatants.

The operation was the first known American-led ground mission in Yemen since December 2014, when members of SEAL Team 6 stormed a village in southern Yemen in an effort to free an American photojournalist held hostage by Al Qaeda. But the raid ended with the kidnappers killing the journalist and a South African held with him.

That mission and the raid over the weekend revealed the shortcomings of secretive military operations in Yemen. The United States was forced to withdraw the last 125 Special Operations advisers from the country in March 2015 after Houthi rebels ousted the government of President Abdu Rabbu Mansour Hadi, the Americans’ main counterterrorism partner.

The loss of Yemen as a base for American counterterrorism training, advising and intelligence-gathering was a significant blow to blunting the advance of Al Qaeda’s branch in the country and keeping tabs on their plots. The Pentagon has tried to start rebuilding its counterterrorism operations in Yemen, however; last year, American Special Operations forces helped Emirati troops evict Qaeda fighters from the port city of Mukalla.

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