Crispr Molecular System Allows Scientists to Edit Genes

CrisprEditsGenes2014-04-28.jpgSource of graph: online version of the NYT article quoted and cited below.

(p. D1) In the late 1980s, scientists at Osaka University in Japan noticed unusual repeated DNA sequences next to a gene they were studying in a common bacterium. They mentioned them in the final paragraph of a paper: “The biological significance of these sequences is not known.”
Now their significance is known, and it has set off a scientific frenzy.
The sequences, it turns out, are part of a sophisticated immune system that bacteria use to fight viruses. And that system, whose very existence was unknown until about seven years ago, may provide scientists with unprecedented power to rewrite the code of life.
In the past year or so, researchers have discovered that the bacterial system can be harnessed to make precise changes to the DNA of humans, as well as other animals and plants.
This means a genome can be edited, much as a writer might change words or fix spelling errors. It allows “customizing the genome of any cell or any species at will,” said Charles Gersbach, an assistant professor of biomedical engineering at Duke University.

For the full story, see:
ANDREW POLLACK. “A Powerful New Way to Edit DNA.” The New York Times (Tues., MARCH 4, 2014): D1 & D5.
(Note: the online version of the story has the date MARCH 3, 2014.)

30,000 Year Old Virus Revived from Permafrost

(p. D5) From Siberian permafrost more than 30,000 years old, [French and Russian researchers] have revived a virus that’s new to science.
“To pull out a virus that’s 30,000 years old and actually grow it, that’s pretty impressive,” said Scott O. Rogers of Bowling Green State University who was not involved in the research. “This goes well beyond what anyone else has done.”
. . .
Measuring 1.5 micrometers long, the viruses are 25 percent bigger than any virus previously found.
. . .
“Sixty percent of its gene content doesn’t resemble anything on earth,” Dr. Abergel said. She and her colleagues suspect that pithoviruses may be parasitic survivors of life forms that were very common early in the history of life.
. . .
“Its potential implications for evolutionary theory and health are quite astonishing,” said Eske Willerslev, an evolutionary biologist at the University of Copenhagen.

For the full story, see:
Carl Zimmer. “Out of Siberian Ice, a Virus Revived.” The New York Times (Tues., MARCH 4, 2014): D5.
(Note: ellipses, and bracketed words, added.)
(Note: the online version of the story has the date MARCH 3, 2014.)

In France “‘Liberté, Égalité, Fraternité’ Means that What’s Yours Should Be Mine”

SantacruzGuillaumeFrenchEntrepreneurInLondon2014-04-27.jpgGuillaume Santacruz is among many French entrepreneurs now using London as their base. He said of his native France, “The economy is not going well, and if you want to get ahead or run your own business, the environment is not good.” Source of caption and photo: online version of the NYT article quoted and cited below.

(p. 1) Guillaume Santacruz, an aspiring French entrepreneur, brushed the rain from his black sweater and skinny jeans and headed down to a cavernous basement inside Campus London, a seven-story hive run by Google in the city’s East End.
. . .
A year earlier, Mr. Santacruz, who has two degrees in finance, was living in Paris near the Place de la Madeleine, working in a boutique finance firm. He had taken that job after his attempt to start a business in Marseille foundered under a pile of government regulations and a seemingly endless parade of taxes. The episode left him wary of starting any new projects in France. Yet he still hungered to be his own boss.
He decided that he would try again. Just not in his own country.
“A lot of people are like, ‘Why would you ever leave France?’ ” Mr. Santacruz said. “I’ll tell you. France has a lot of problems. There’s a feeling of gloom that seems to be growing deeper. The economy is not going well, and if you want to get ahead or run your own business, the environment is not good.”
. . .
(p. 5) “Making it” is almost never easy, but Mr. Santacruz found the French bureaucracy to be an unbridgeable moat around his ambitions. Having received his master’s in finance at the University of Nottingham in England, he returned to France to work with a friend’s father to open dental clinics in Marseille. “But the French administration turned it into a herculean effort,” he said.
A one-month wait for a license turned into three months, then six. They tried simplifying the corporate structure but were stymied by regulatory hurdles. Hiring was delayed, partly because of social taxes that companies pay on salaries. In France, the share of nonwage costs for employers to fund unemployment benefits, education, health care and pensions is more than 33 percent. In Britain, it is around 20 percent.
“Every week, more tax letters would come,” Mr. Santacruz recalled.
. . .
Diane Segalen, an executive recruiter for many of France’s biggest companies who recently moved most of her practice, Segalen & Associés, to London from Paris, says the competitiveness gap is easy to see just by reading the newspapers. “In Britain, you read about all the deals going on here,” Ms. Segalen said. “In the French papers, you read about taxes, more taxes, economic problems and the state’s involvement in everything.”
. . .
“It is a French cultural characteristic that goes back to almost the revolution and Robespierre, where there’s a deep-rooted feeling that you don’t show that you make money,” Ms. Segalen, the recruiter, said. “There is this sense that ‘liberté, égalité, fraternité’ means that what’s yours should be mine. It’s more like, if someone has something I can’t have, I’d rather deprive this person from having it than trying to work hard to get it myself. That’s a very French state of mind. But it’s a race to the bottom.”

For the full story, see:
LIZ ALDERMAN. “Au Revoir, Entrepreneurs.” The New York Times, SundayBusiness Section (Sun., MARCH 23, 2014): 1 & 5.
(Note: ellipses added.)
(Note: the online version of the story has the date MARCH 22, 2014.)

SegalenDianeFrenchEntrepreneurInLondon2014-04-27.jpg ‘Diane Segalen moved most of her executive recruiting practice to London from Paris. In France, she says, “there is this sense that ‘liberté, égalité, fraternité’ means that what’s yours should be mine.”” Source of caption and photo: online version of the NYT article quoted and cited above.

Heart Pioneer Bailey Kept Moving from Hospital to Hospital Due to His Failures

ExtemeMedicineBK2014-04-25.jpg

Source of book image:
http://media.npr.org/assets/bakertaylor/covers/e/extreme-medicine/9781594204708_custom-14713d8588e54f066a6abf7b5a13e4c9de832ea1-s6-c30.jpg

(p. C8) In “Extreme Medicine,” physician Kevin Fong reminds us that virtually everything we take for granted in lifesaving medical intervention was once unthinkable. Over the past century, as technology has allowed man to conquer hostile environments and modernize warfare, medical pioneers have been on a parallel journey, confronting what had once been fatal in man’s boldest pursuits and making it survivable.
. . .
As Dr. Fong notes, many of today’s commonplace treatments were once dangerously experimental. One pioneer in the early postwar years, a Philadelphia surgeon named Charles Bailey, killed several patients while trying to repair problems of the mitral valve, which if damaged can cause blood to flow backward into the hear chamber, decreasing flow to the rest of the body. Bailey moved from hospital to hospital to avoid scrutiny of his successive failures.

For the full review, see:
LAURA LANDRO. “BOOKS; They Died So We Might Live; Hypothermia, which killed explorers like Scott, is now induced in heart patients to allow time for surgery.” The Wall Street Journal (Sat., Feb. 15, 2014): C8.
(Note: ellipsis added.)
(Note: the online version of the review has the date Feb. 14, 2014, and has the title “BOOKSHELF; Book Review: ‘Extreme Medicine’ by Kevin Fong; Explorers, astronauts and soldiers all pushed the limits of doctors’ abilities to heal and repair.”)

The book under review is:
Swidey, Neil. Trapped under the Sea: One Engineering Marvel, Five Men, and a Disaster Ten Miles into the Darkness. New York: Crown Publishers, 2014.

Sweden Shows ObamaCare Will Cause Health Care Delays and Rationing

(p. A11) President Obama has declared the Affordable Care Act a success–a reform that is “here to stay.” The question remains, however: What should we expect to come out of it, and do we want the effects to stay? If the experiences of Sweden and other countries with universal health care are any indication, patients will soon start to see very long wait times and difficulty getting access to care.
. . .
Rationing is an obvious effect of economic planning in place of free-market competition. Free markets allow companies and entrepreneurs to respond to demand by offering people what they want and need at a better price. Effective and affordable health care comes from decentralized innovation and risk-taking as well as freedom in pricing and product development. The Affordable Care Act does the opposite by centralizing health care, minimizing or prohibiting differentiation in pricing and offerings, and mandating consumers to purchase insurance. It effectively overrides the market and the signals it sends about supply and demand.
Stories of people in Sweden suffering stroke, heart failure and other serious medical conditions who were denied or unable to receive urgent care are frequently reported in Swedish media. Recent examples include a one-month-old infant with cerebral hemorrhage for whom no ambulance was made available, and an 80-year-old woman with suspected stroke who had to wait four hours for an ambulance.
Other stories include people waiting many hours before a nurse or anyone talked to them after they arrived in emergency rooms and then suffering for long periods of time before receiving needed care. A 42-year-old woman in Karlstad seeking care for meningitis died in the ER after a three-hour wait. A woman with colon cancer spent 12 years contesting a money-saving decision to deny an abdominal scan that would have found the cancer earlier. The denial-of-care decision was not made by an insurance company, but by the government health-care system and its policies.

For the full commentary, see:
PER BYLUND. “OPINION; What Sweden Can Teach Us About ObamaCare; Universal public health care means the average Swede with ‘high risk’ prostate cancer waits 220 days for treatment.” The Wall Street Journal (Fri., April 18, 2014): A11.
(Note: ellipsis added.)
(Note: the online version of the commentary has the date April 17, 2014.)

Research on Dogs that Benefits Both Humans and Dogs

MooreEricaExaminesAkyra2014-04-24.jpg “Erica Moore examined Akyra, a shih tzu, in August before the dog was enrolled in Penn Vet’s canine mammary tumor program. She had surgery there.” Source of caption and photo: online version of the NYT article quoted and cited below.

(p. D6) Akyra’s mammary glands were riddled with tumors, including one the size of a golf ball. She would be hard to place in a home, and the medical care she needed would be expensive. The tumors could be cancerous.

“When my husband called and said they were going to leave one of the dogs behind because she had mammary tumors, I said, ‘No, you’re not!’ ” said Bekye Eckert, 49, a dog lover who lives outside Baltimore and has cared for several animals with mammary cancer.
Ms. Eckert arranged for Akyra to be enrolled in an innovative program at the University of Pennsylvania, where veterinary oncologists are learning about the progression of human breast cancer by treating mammary tumors in shelter dogs.
. . .
Generally, two sets of tumor samples are taken from each dog, one for the pathology lab and one for Dr. Troyanskaya to use for molecular analysis. Astrid, for example, had tumors in seven mammary glands that were mostly benign. The largest proved to be malignant.
Such a large set of samples is a gold mine for Dr. Troyanskaya, who is looking for changes in the expression of a specific gene or group of genes, or pathways linking groups of genes as the tumor becomes malignant.
. . .
In the meantime, stray dogs are getting free cancer treatment that makes it easier to find them permanent homes, and they are promised care for any recurrence. More than 100 dogs have been through the program; several have been adopted by women who also survived breast cancer.
For Akyra, there was good news. She had surgery in August, and veterinarians removed the large tumor and three smaller lesions. The pathology report gave her a clean bill of health: None were cancerous. She was adopted by Beth Gardner, a relocation consultant in Devon, Pa.

For the full story, see:
RONI CARYN RABIN. “By Treating Dogs, Answers About Breast Cancer.” The New York Times (Tues., April 1, 2014): D6.
(Note: ellipses added.)
(Note: the online version of the commentary has the date MARCH 31, 2014, and has the title “From Dogs, Answers About Breast Cancer.”)

Re-Use of Plastic Bags Increases E. Coli Infections

(p. A13) Though reducing plastic-bag use might be good for the environment, encouraging the re-use of plastic bags for food-toting may not be so healthy for humans. After San Francisco introduced its ban on non-compostable plastic bags in large grocery stores in 2007, researchers discovered a curious spike in E. coli infections, which can be fatal, and a 46% increase in deaths from food-borne illnesses, according to a study published in November 2012 by the University of Pennsylvania and George Mason University. “We show that the health costs associated with the San Francisco ban swamp any budgetary savings from reduced litter,” the study’s authors observed.
Affirming this yuck factor, a 2011 study from the University of Arizona and Loma Linda University found bacteria in 99% of reusable polypropylene bags tested; 8% of them were carrying E. coli. The study, though it mainly focused on plastic bags, also looked at two cotton reusable bags–and both contained bacteria.
Bag-ban boosters counter that consumers just need to wash their bags and use separate bags for fish and meat. If only my washing machine had a “reusable bag vinegar rinse cycle.” A paltry 3% of shoppers surveyed in that same 2011 study said they washed their reusable bags. Has anybody calculated the environmental impact of drought-ravaged Californians laundering grocery bags?

For the full commentary, see:
JUDY GRUEN. “Becoming a Bagless Lady in Los Angeles.” The Wall Street Journal (Sat., March 8, 2014): A13.
(Note: the online version of the commentary has the date March 7, 2014.)

The 2012 study mistakenly labelled above as “published” is:
Klick, Jonathan and Wright, Joshua D., Grocery Bag Bans and Foodborne Illness (November 2, 2012). U of Penn, Inst for Law & Econ Research Paper No. 13-2. Available at SSRN: http://ssrn.com/abstract=2196481 or http://dx.doi.org/10.2139/ssrn.2196481

The 2011 article mentioned above, is:
Williams, David L., Charles P. Gerba, Sherri Maxwell, and Ryan G. Sinclair. “Assessment of the Potential for Cross-Contamination of Food Products by Reusable Shopping Bags.” Food Protection Trends 31, no. 8 (Aug. 2011): 508-13.

Solitary Swimming Helps Creativity and Problem-Solving

(p. 5) Ms. Nyad has spent a lifetime in the water, chasing an elusive mark in marathon swimming, and she has written about the exhilarating out-of-body experience she has when powering through long distances. The medium makes it necessary to unplug; the blunting of the senses by water encourages internal retreat. Though we don’t all reach nirvana when we swim, swimming may well be that last refuge from connectivity — and, for some, the only way to find the solitary self.
. . .
For better or worse, the mind wanders: We are left alone with our thoughts, wherever they may take us. A lot of creative thinking happens when we’re not actively aware of it. A recent Carnegie Mellon study shows that to make good decisions, our brains need every bit of that room to meander. Other research has found that problem-solving tends to come most easily when our minds are unfocused, and while we’re exercising. The neurologist Oliver Sacks has written books in his head while swimming. “Theories and stories would construct themselves in my mind as I swam to and fro, or round and round Lake Jeff,” he writes in the essay “Water Babies.” Five hundred lengths in a pool were never boring or monotonous; instead, Dr. Sacks writes, “swimming gave me a sort of joy, a sense of well-being so extreme that it became at times a sort of ecstasy.” The body is engaged in full physical movement, but the mind itself floats, untethered. Beyond this, he adds, “there is all the symbolism of swimming — its imaginative resonances, its mythic potentials.”
Dr. Sacks describes a sublime state that is accessible to all, from his father, with his “great whalelike bulk,” who swam daily and elegantly until 94 years of age, to the very young.   . . .
. . .
I asked Dara Torres, who has logged countless training hours for her five Olympics, what she thinks about when she’s swimming. “I’m always doing five things at once,” she told me by phone (at the time, she was driving a car). “So when I get in the water, I think about all the things that I have to do. But sometimes I go into a state — I don’t really think about anything.” The important thing, she says, is that the time is yours. “You can use it for anything. It depends where your head is at — it’s a reflection of where you are.”
The reflection of where you are: in essence, a status update to you, and only you. The experience is egalitarian. You don’t have to be a great swimmer to appreciate the benefits of sensory solitude and the equilibrium the water can bring.

For the full commentary, see:
Justin Gillis. “BY DEGREES; Freezing Out the Bigger Picture.” The New York Times (Tues., FEB. 11, 2014): D3.
(Note: ellipses added.)
(Note: the online version of the commentary has the date FEB. 10, 2014.)

Some Geographical Clusters Are Due to Chance (It Is Not Always a Miracle, When Good, Or the Environment, When Bad)

HandDavidStatistiician2014-04-04.jpg

David J. Hand. Source of photo: online version of the NYT article quoted and cited below.

(p. 12) Your latest book, “The Improbability Principle,” aims to prove that extremely improbable events are in fact commonplace. Can you explain that a bit? Things like roulette wheels coming up in strange configurations or the same lottery numbers hitting two weeks in a row are clearly very rare events, but if you look at the number of lotteries and the number of roulette wheels, then you realize that you should actually expect these sorts of things to happen. I think within the statistical community people accept this. They’re aware of the impact of the law of truly large numbers.
. . .
You also write that geographical clusters of people with diseases might not necessarily be a result of environmental issues. It could just be a coincidence. Well, they could be due to some sort of pollution or infectious disease or something like that, but you can expect clusters to occur just by chance as well. So it’s an interesting statistical problem to tease these things out. Is this a genuine cluster in the sense that there’s a cause behind it? Or is it a chance cluster?

For the full interview, see:
Chozick, Amy, interviewer. “‘The Wonder Is Still There’; The Statistician David J. Hand on Eerie Coincidences and Playing the Lottery.” The New York Times Magazine (Sun., FEB. 23, 2014): 12.
(Note: ellipsis added; bold in original.)
(Note: the online version of the interview has the date FEB. 21, 2014, and has the title “David J. Hand’s Lottery Tips.”)

Hand’s book is:
Hand, David J. The Improbability Principle: Why Coincidences, Miracles, and Rare Events Happen Every Day. New York: Scientific American/Farrar, Straus and Giroux, 2014.

If Lack of Focus and Poverty Go Together, Which Is the Cause and Which the Effect?

ScarcityBK2014-03-06.jpg

Source of book image: http://www.scientificamerican.com/sciam/cache/file/BF860CC7-371A-46BB-8ACCECD4289565A8.jpg

Are the poor poor partly because they concentrate less, or do they concentrate less partly because they are poor? Samantha Power discusses one of her favorite books of 2013:

(p. C11) In “Scarcity,” Sendhil Mullainathan and Eldar Shafir offer groundbreaking insights into, among other themes, the effects of poverty on (p. C12) cognition and our ability to make choices about our lives. The authors persuasively show that the mental space–or “bandwidth”–of the poor is so consumed with making ends meet that they may be more likely to lose concentration while on a job or less likely to take medication on time.

For the full article, see:
“12 Months of Reading; We asked 50 of our friends–from April Bloomfield to Mike Tyson–to name their favorite books of 2013.” The Wall Street Journal (Sat., Dec. 14, 2013): C6 & C9-C12.
(Note: the online version of the article has the date Dec. 13, 2013.)

The book that Power praises is:
Mullainathan, Sendhil, and Eldar Shafir. Scarcity: Why Having Too Little Means So Much. New York: Times Books, 2013.

Regulators Forbid Doctor from Curing Dentist’s Pelvic Pain

DavidsonDaneilPelvicPain2014-01-16.jpg “Dr. Daniel Davidson, an Idaho dentist, has pelvic pain so severe that he cannot sit, and can stand for only limited periods.” Source of caption and photo: online version of the NYT article quoted and cited below.

(p. A18) After visiting dozens of doctors and suffering for nearly five years from pelvic pain so severe that he could not work, Daniel Davidson, 57, a dentist in Dalton Gardens, Idaho, finally found a specialist in Phoenix who had an outstanding reputation for treating men like him.

Dr. Davidson, whose pain followed an injury, waited five months for an appointment and even rented an apartment in Phoenix, assuming he would need surgery and time to recover.
Six days before the appointment, it was canceled. The doctor, Michael Hibner, an obstetrician-gynecologist at St. Joseph’s Hospital and Medical Center, had learned that members of his specialty were not allowed to treat men and that if he did so, he could lose his board certification — something that doctors need in order to work.
The rule had come from the American Board of Obstetrics and Gynecology. On Sept. 12, it posted on its website a newly stringent and explicit statement of what its members could and could not do. Except for a few conditions, gynecologists were prohibited from treating men. Pelvic pain was not among the exceptions.
Dr. Davidson went home, close to despair. His condition has left him largely bedridden. The pain makes it unbearable for him to sit, and he can stand for only limited periods before he needs to lie down.
“These characters at the board jerked the rug out from underneath me,” he said.

For the full story, see:
DENISE GRADY. “Men With Pelvic Pain Find a Path to Treatment Blocked by a Gynecology Board.” The New York Times (Weds., December 11, 2013): A18.
(Note: the online version of the story has the date December 10, 2013.)