Ramblings of a Conuly

Wed, 22 May 2013 13:20:32 GMT

Wells Dry, Fertile Plains Turn to Dust

http://nyti.ms/18OrdKk

HASKELL COUNTY, Kan. — Forty-nine years ago, Ashley Yost’s grandfather sank a well deep into a half-mile square of rich Kansas farmland. He struck an artery of water so prodigious that he could pump 1,600 gallons to the surface every minute.

Last year, Mr. Yost was coaxing just 300 gallons from the earth, and pumping up sand in order to do it. By harvest time, the grit had robbed him of $20,000 worth of pumps and any hope of returning to the bumper harvests of years past.

“That’s prime land,” he said not long ago, gesturing from his pickup at the stubby remains of last year’s crop. “I’ve raised 294 bushels of corn an acre there before, with water and the Lord’s help.” Now, he said, “it’s over.”

The land, known as Section 35, sits atop the High Plains Aquifer, a waterlogged jumble of sand, clay and gravel that begins beneath Wyoming and South Dakota and stretches clear to the Texas Panhandle. The aquifer’s northern reaches still hold enough water in many places to last hundreds of years. But as one heads south, it is increasingly tapped out, drained by ever more intensive farming and, lately, by drought.

Vast stretches of Texas farmland lying over the aquifer no longer support irrigation. In west-central Kansas, up to a fifth of the irrigated farmland along a 100-mile swath of the aquifer has already gone dry. In many other places, there no longer is enough water to supply farmers’ peak needs during Kansas’ scorching summers.

And when the groundwater runs out, it is gone for good. Refilling the aquifer would require hundreds, if not thousands, of years of rains.

This is in many ways a slow-motion crisis — decades in the making, imminent for some, years or decades away for others, hitting one farm but leaving an adjacent one untouched. But across the rolling plains and tarmac-flat farmland near the Kansas-Colorado border, the effects of depletion are evident everywhere. Highway bridges span arid stream beds. Most of the creeks and rivers that once veined the land have dried up as 60 years of pumping have pulled groundwater levels down by scores and even hundreds of feet.

On some farms, big center-pivot irrigators — the spindly rigs that create the emerald circles of cropland familiar to anyone flying over the region — now are watering only a half-circle. On others, they sit idle altogether.

Two years of extreme drought, during which farmers relied almost completely on groundwater, have brought the seriousness of the problem home. In 2011 and 2012, the Kansas Geological Survey reports, the average water level in the state’s portion of the aquifer dropped 4.25 feet — nearly a third of the total decline since 1996.

And that is merely the average. “I know my staff went out and re-measured a couple of wells because they couldn’t believe it,” said Lane Letourneau, a manager at the State Agriculture Department’s water resources division. “There was a 30-foot decline.”

Kansas agriculture will survive the slow draining of the aquifer — even now, less than a fifth of the state’s farmland is irrigated in any given year — but the economic impact nevertheless will be outsized. In the last federal agriculture census of Kansas, in 2007, an average acre of irrigated land produced nearly twice as many bushels of corn, two-thirds more soybeans and three-fifths more wheat than did dry land.

Farmers will take a hit as well. Raising crops without irrigation is far cheaper, but yields are far lower. Drought is a constant threat: the last two dry-land harvests were all but wiped out by poor rains.

In the end, most farmers will adapt to farming without water, said Bill Golden, an agriculture economist at Kansas State University. “The revenue losses are there,” he said. “But they’re not as tremendously significant as one might think.”

Some already are. A few miles west of Mr. Yost’s farm, Nathan Kells cut back on irrigation when his wells began faltering in the last decade, and shifted his focus to raising dairy heifers — 9,000 on that farm, and thousands more elsewhere. At about 12 gallons a day for a single cow, Mr. Kells can sustain his herd with less water than it takes to grow a single circle of corn.

“The water’s going to flow to where it’s most valuable, whether it be industry or cities or feed yards,” he said. “We said, ‘What’s the higher use of the water?’ and decided that it was the heifer operation.”

The problem, others say, is that when irrigation ends, so do the jobs and added income that sustain rural communities.

“Looking at areas of Texas where the groundwater has really dropped, those towns are just a shell of what they once were,” said Jim Butler, a hydrogeologist and senior scientist at the Kansas Geological Survey.

The villain in this story is in fact the farmers’ savior: the center-pivot irrigator, a quarter- or half-mile of pipe that traces a watery circle around a point in the middle of a field. The center pivots helped start a revolution that raised farming from hardscrabble work to a profitable business.

Since the pivots’ debut some six decades ago, the amount of irrigated cropland in Kansas has grown to nearly three million acres, from a mere 250,000 in 1950. But the pivot irrigators’ thirst for water — hundreds and sometimes thousands of gallons a minute — has sent much of the aquifer on a relentless decline. And while the big pivots have become much more efficient, a University of California study earlier this year concluded that Kansas farmers were using some of their water savings to expand irrigation or grow thirstier crops, not to reduce consumption.

A shift to growing corn, a much thirstier crop than most, has only worsened matters. Driven by demand, speculation and a government mandate to produce biofuels, the price of corn has tripled since 2002, and Kansas farmers have responded by increasing the acreage of irrigated cornfields by nearly a fifth.

At an average 14 inches per acre in a growing season, a corn crop soaks up groundwater like a sponge — in 2010, the State Agriculture Department said, enough to fill a space a mile square and nearly 2,100 feet high.

Sorghum, or milo, gets by on a third less water, Kansas State University researchers say — and it, too, is in demand by biofuel makers. As Kansas’ wells peter out, more farmers are switching to growing milo on dry land or with a comparative sprinkle of irrigation water.

But as long as there is enough water, most farmers will favor corn. “The issue that often drives this is economics,” said David W. Hyndman, who heads Michigan State University’s geological sciences department. “And as long as you’ve got corn that’s $7, then a lot of choices get made on that.”

Of the 800 acres that Ashley Yost farmed last year in Haskell County, about 70 percent was planted in corn, including roughly 125 acres in Section 35. Haskell County’s feedlots — the county is home to 415,000 head of cattle — and ethanol plants in nearby Liberal and Garden City have driven up the price of corn handsomely, he said.

But this year he will grow milo in that section, and hope that by ratcheting down the speed of his pump, he will draw less sand, even if that means less water, too. The economics of irrigation, he said, almost dictate it.

“You’ve got $20,000 of underground pipe,” he said. “You’ve got a $10,000 gas line. You’ve got a $10,000 irrigation motor. You’ve got an $89,000 pivot. And you’re going to let it sit there and rot?

“If you can pump 150 gallons, that’s 150 gallons Mother Nature is not giving us. And if you can keep a milo crop alive, you’re going to do it.”

Mr. Yost’s neighbors have met the prospect of dwindling water in starkly different ways. A brother is farming on pivot half-circles. A brother-in-law moved most of his operations to Iowa. Another farmer is suing his neighbors, accusing them of poaching water from his slice of the aquifer.

A fourth grows corn with an underground irrigation system that does not match the yields of water-wasting center-pivot rigs, but is far thriftier in terms of water use and operating costs.

For his part, Mr. Yost continues to pump. But he also allowed that the day may come when sustaining what is left of the aquifer is preferable to pumping as much as possible.

Sitting in his Ford pickup next to Section 35, he unfolded a sheet of white paper that tracked the decline of his grandfather’s well: from 1,600 gallons a minute in 1964, to 1,200 in 1975, to 750 in 1976.

When the well slumped to 500 gallons in 1991, the Yosts capped it and drilled another nearby. Its output sank, too, from 1,352 gallons to 300 today.

This year, Mr. Yost spent more than $15,000 to drill four test wells in Section 35. The best of them produced 195 gallons a minute — a warning, he said, that looking further for an isolated pocket of water would be costly and probably futile.

“We’re on the last kick,” he said. “The bulk water is gone.”

Why No Safe Room to Run To? Cost and Plains Culture

http://nyti.ms/10NPJIh

The Web site for the City of Moore, Okla., recommends “that every residence have a storm safe room or an underground cellar.” It says below-ground shelters are the best protection against tornadoes.

But no local ordinance or building code requires such shelters, either in houses, schools or businesses, and only about 10 percent of homes in Moore have them.

Nor does the rest of Oklahoma, one of the states in the storm belt called Tornado Alley, require them — despite the annual onslaught of deadly and destructive twisters like the one on Monday, which killed at least 24 people, injured hundreds and eliminated entire neighborhoods.

It is a familiar story, as well, in places like Joplin, Mo., and across the Great Plains and in the Deep South, where tornadoes are a seasonal threat but government regulation rankles.

In 2011, a monster tornado razed large parts of Joplin, killing 160 people in a state that had no storm-shelter requirements. The city considered requiring shelters in rebuilt or new homes but decided that doing so would be “cost prohibitive” because the soil conditions make building basements expensive, said the assistant city manager, Sam Anselm. Even so, he estimated that half the homes that had been rebuilt included underground shelters. Schools were being rebuilt with safe rooms, he said.

In Moore, the Web site explains that the city has no community shelter because a 15-minute warning is not enough time to get to safety and because, “overall, people face less risk by taking shelter in a reasonably well-constructed residence.”

This is generally true, but not for a storm like Monday’s milewide tornado, which was a terrible reminder of a tornado that caused extensive damage on May 3, 1999.

Curtis McCarty, a member of the Oklahoma Uniform Building Code Commission and a builder himself, said the twister on Monday would have defeated attempts to resist it above ground. “You cannot build a structure that’s going to take a direct hit from a tornado like that that’s going to stand,” he said.

The city’s Web site sounds tones that, in retrospect, might seem implausibly optimistic. It says the experience in 1999 — “an extremely unique event weatherwise” — meant that the standard “shelter in place” methods of protection were adequate. If another storm comes, “there’s only a less than 1 percent chance of it being as strong and violent as what we experienced” before.

Larry Graves, a project manager with Downey Consulting, an engineering company in Oklahoma City that works with schools, said buildings had been upgraded with safe rooms in a piecemeal way in recent years. “You’re seeing more of it, but it’s a big funding item,” he said, noting that a school district might reinforce a large common bathroom with concrete or build an extra-strong gymnasium as a shelter.

Without added protection, Mr. Graves said, the drill is roughly the same as it was when he was a schoolboy 40 years ago: “They move you into the hallway, and you stay there tucked up and wait it out.”

Construction standards in Moore have been studied extensively. In a 2002 study published in the journal of the American Meteorological Society, Timothy P. Marshal, an engineer in Dallas, suggested that “the quality of new home construction generally was no better than homes built prior to the tornado” in 1999.

Few homes built in the town after the storm were secured to their foundations with bolted plates, which greatly increase resistance to storms; instead, most were secured with the same kinds of nails and pins that failed in 1999. Just 6 of 40 new homes had closet-size safe rooms.

Mayor Glenn Lewis of Moore said that since then, the town had strengthened building codes, including a requirement that new homes incorporate hurricane braces. The city has also aggressively promoted the construction of safe rooms and other measures, with more than $12 million from state and federal emergency management funds to subsidize safe-room construction by offering a $2,000 rebate, said Albert Ashwood, the director of the Oklahoma Department of Emergency Management. Still, he said, it has been several years since Moore has received new financing for the program.

About a year and a half ago, Mr. McCarty, the builder, spoke to a group of Oklahoma legislators who were considering mandating shelters for new homes, he recalled. But no legislation was proposed, he said, because of the bad economy. A small, prefabricated sunken shelter can cost $4,000, he said, and “mandating another three or four thousand dollars on every new home can really add up when you’re trying to keep houses affordable.”

Houses in Oklahoma, Mr. McCarty said, are usually built on slabs without basements or crawl spaces because the land is flat and the weather is temperate enough that digging a deep foundation is not necessary, as it is with homes built in the Northeast, where the temperatures regularly dip below freezing.

“When you look at the flat land, and the amount it would cost to excavate and remove the dirt, the cost of the foundation to build a basement just adds a substantial amount to the cost of a new home,” Mr. McCarty said.

Assessment calculations also discourage basement building, he said; assessors value basement square footage at half the rate of ground-level space.

Mike Gilles, a former president of the Oklahoma State Home Builders Association, said that he built safe rooms in all his custom homes, and that even many builders who build speculatively now make them standard.

But asked whether the government should require safe rooms in homes, he said, “Most homebuilders would be against that because we think the market ought to drive what people are putting in the houses, not the government.”

Mr. Anselm, the official in Joplin, said that the city had applied to Missouri for emergency funds for safe rooms, but that the state used money from the Federal Emergency Management Agency primarily for disaster relief from flooding.

Beyond expense and construction standards, there is a local attitude about tornadoes that borders on temerity. There is a joke among Oklahomans that when the storm sirens sound, instead of taking cover, everyone goes outside and looks for the storm.

That was what Leon and Larry Harjo did Monday. The 45-year-old twins sat outside their brick home to see what was going on as the sirens blared and hailstones pelted. Only when they glimpsed the enormous funnel cloud barreling their way did they run to a medical center across the street to take cover in a hallway.

Even that was a harrowing experience; Larry Harjo said the wind had blown him and his wife around as they clutched each other on the ground. A door was ripped off its hinges, ceiling tiles fell, and they heard cars crashing against the building.

Would surviving the tornado make them think twice about waiting so long to hunker down the next time?

Larry Harjo said: “You can’t run every time you hear a warning. You’ll be scared your whole life.”

His brother added: “Might as well just sit back. If it gets you, it gets you. If not, another day.”

Just finished up a game of Bohnanza with everybody.

Mon, 20 May 2013 02:22:38 GMT

Are the girls, who haven't played before, allowed to thoroughly trounce the adults? It seems unfair somehow, and I know we weren't letting them win! I really have no idea how they did it, they didn't even collude with each other as they usually do when playing games!

Say Hello to the 100 Trillion Organisms That Make Up Your Microbiome

Sun, 19 May 2013 17:31:58 GMT

http://nyti.ms/15Mgstn

I can tell you the exact date that I began to think of myself in the first-person plural — as a superorganism, that is, rather than a plain old individual human being. It happened on March 7. That’s when I opened my e-mail to find a huge, processor-choking file of charts and raw data from a laboratory located at the BioFrontiers Institute at the University of Colorado, Boulder. As part of a new citizen-science initiative called the American Gut project, the lab sequenced my microbiome — that is, the genes not of “me,” exactly, but of the several hundred microbial species with whom I share this body. These bacteria, which number around 100 trillion, are living (and dying) right now on the surface of my skin, on my tongue and deep in the coils of my intestines, where the largest contingent of them will be found, a pound or two of microbes together forming a vast, largely uncharted interior wilderness that scientists are just beginning to map.

I clicked open a file called Taxa Tables, and a colorful bar chart popped up on my screen. Each bar represented a sample taken (with a swab) from my skin, mouth and feces. For purposes of comparison, these were juxtaposed with bars representing the microbiomes of about 100 “average” Americans previously sequenced.

Here were the names of the hundreds of bacterial species that call me home. In sheer numbers, these microbes and their genes dwarf us. It turns out that we are only 10 percent human: for every human cell that is intrinsic to our body, there are about 10 resident microbes — including commensals (generally harmless freeloaders) and mutualists (favor traders) and, in only a tiny number of cases, pathogens. To the extent that we are bearers of genetic information, more than 99 percent of it is microbial. And it appears increasingly likely that this “second genome,” as it is sometimes called, exerts an influence on our health as great and possibly even greater than the genes we inherit from our parents. But while your inherited genes are more or less fixed, it may be possible to reshape, even cultivate, your second genome.

Justin Sonnenburg, a microbiologist at Stanford, suggests that we would do well to begin regarding the human body as “an elaborate vessel optimized for the growth and spread of our microbial inhabitants.” This humbling new way of thinking about the self has large implications for human and microbial health, which turn out to be inextricably linked. Disorders in our internal ecosystem — a loss of diversity, say, or a proliferation of the “wrong” kind of microbes — may predispose us to obesity and a whole range of chronic diseases, as well as some infections. “Fecal transplants,” which involve installing a healthy person’s microbiota into a sick person’s gut, have been shown to effectively treat an antibiotic-resistant intestinal pathogen named C. difficile, which kills 14,000 Americans each year. (Researchers use the word “microbiota” to refer to all the microbes in a community and “microbiome” to refer to their collective genes.) We’ve known for a few years that obese mice transplanted with the intestinal community of lean mice lose weight and vice versa. (We don’t know why.) A similar experiment was performed recently on humans by researchers in the Netherlands: when the contents of a lean donor’s microbiota were transferred to the guts of male patients with metabolic syndrome, the researchers found striking improvements in the recipients’ sensitivity to insulin, an important marker for metabolic health. Somehow, the gut microbes were influencing the patients’ metabolisms.

Our resident microbes also appear to play a critical role in training and modulating our immune system, helping it to accurately distinguish between friend and foe and not go nuts on, well, nuts and all sorts of other potential allergens. Some researchers believe that the alarming increase in autoimmune diseases in the West may owe to a disruption in the ancient relationship between our bodies and their “old friends” — the microbial symbionts with whom we coevolved.

These claims sound extravagant, and in fact many microbiome researchers are careful not to make the mistake that scientists working on the human genome did a decade or so ago, when they promised they were on the trail of cures to many diseases. We’re still waiting. Yet whether any cures emerge from the exploration of the second genome, the implications of what has already been learned — for our sense of self, for our definition of health and for our attitude toward bacteria in general — are difficult to overstate. Human health should now “be thought of as a collective property of the human-associated microbiota,” as one group of researchers recently concluded in a landmark review article on microbial ecology — that is, as a function of the community, not the individual.

Such a paradigm shift comes not a moment too soon, because as a civilization, we’ve just spent the better part of a century doing our unwitting best to wreck the human-associated microbiota with a multifronted war on bacteria and a diet notably detrimental to its well-being. Researchers now speak of an impoverished “Westernized microbiome” and ask whether the time has come to embark on a project of “restoration ecology” — not in the rain forest or on the prairie but right here at home, in the human gut.

In March I traveled to Boulder to see the Illumina HiSeq 2000 sequencing machine that had shed its powerful light on my own microbiome and to meet the scientists and computer programmers who were making sense of my data. The lab is headed by Rob Knight, a rangy, crew-cut 36-year-old biologist who first came to the United States from his native New Zealand to study invasive species, a serious problem in his home country. Knight earned his Ph.D. in ecology and evolutionary biology from Princeton when he was 24 and then drifted from the study of visible species and communities to invisible ones. Along the way he discovered he had a knack for computational biology. Knight is regarded as a brilliant analyst of sequencing data, skilled at finding patterns in the flood of information produced by the machines that “batch sequence” all the DNA in a sample and then tease out the unique genetic signatures of each microbe. This talent explains why so many of the scientists exploring the microbiome today send their samples to be sequenced and analyzed by his lab; it is also why you will find Knight’s name on most of the important papers in the field.

Over the course of two days in Boulder, I enjoyed several meals with Knight and his colleagues, postdocs and graduate students, though I must say I was a little taken aback by the table talk. I don’t think I’ve ever heard so much discussion of human feces at dinner, but then one thing these scientists are up to is a radical revaluation of the contents of the human colon. I learned about Knight’s 16-month-old daughter, who has had most of the diapers to which she has contributed sampled and sequenced. Knight said at dinner that he sampled himself every day; his wife, Amanda Birmingham, who joined us one night, told me that she was happy to be down to once a week. “Of course I keep a couple of swabs in my bag at all times,” she said, rolling her eyes, “because you never know.”

A result of the family’s extensive self-study has been a series of papers examining family microbial dynamics. The data helped demonstrate that the microbial communities of couples sharing a house are similar, suggesting the importance of the environment in shaping an individual’s microbiome. Knight also found that the presence of a family dog tended to blend everyone’s skin communities, probably via licking and petting. One paper, titled “Moving Pictures of the Human Microbiome,” tracked the day-to-day shifts in the microbial composition of each body site. Knight produced animations showing how each community — gut, skin and mouth — hosted a fundamentally different cast of microbial characters that varied within a fairly narrow range over time.

Knight’s daily sampling of his daughter’s diapers (along with those of a colleague’s child) also traced the remarkable process by which a baby’s gut community, which in utero is sterile and more or less a blank slate, is colonized. This process begins shortly after birth, when a distinctive infant community of microbes assembles in the gut. Then, with the introduction of solid food and then weaning, the types of microbes gradually shift until, by age 3, the baby’s gut comes to resemble an adult community much like that of its parents.

The study of babies and their specialized diet has yielded key insights into how the colonization of the gut unfolds and why it matters so much to our health. One of the earliest clues to the complexity of the microbiome came from an unexpected corner: the effort to solve a mystery about milk. For years, nutrition scientists were confounded by the presence in human breast milk of certain complex carbohydrates, called oligosaccharides, which the human infant lacks the enzymes necessary to digest. Evolutionary theory argues that every component of mother’s milk should have some value to the developing baby or natural selection would have long ago discarded it as a waste of the mother’s precious resources.

It turns out the oligosaccharides are there to nourish not the baby but one particular gut bacterium called Bifidobacterium infantis, which is uniquely well-suited to break down and make use of the specific oligosaccharides present in mother’s milk. When all goes well, the bifidobacteria proliferate and dominate, helping to keep the infant healthy by crowding out less savory microbial characters before they can become established and, perhaps most important, by nurturing the integrity of the epithelium — the lining of the intestines, which plays a critical role in protecting us from infection and inflammation.

“Mother’s milk, being the only mammalian food shaped by natural selection, is the Rosetta stone for all food,” says Bruce German, a food scientist at the University of California, Davis, who researches milk. “And what it’s telling us is that when natural selection creates a food, it is concerned not just with feeding the child but the child’s gut bugs too.”

Where do these all-important bifidobacteria come from and what does it mean if, like me, you were never breast-fed? Mother’s milk is not, as once was thought, sterile: it is both a “prebiotic” — a food for microbes — and a “probiotic,” a population of beneficial microbes introduced into the body. Some of them may find their way from the mother’s colon to her milk ducts and from there into the baby’s gut with its first feeding. Because designers of infant formula did not, at least until recently, take account of these findings, including neither prebiotic oligosaccharides or probiotic bacteria in their formula, the guts of bottle-fed babies are not optimally colonized.

Most of the microbes that make up a baby’s gut community are acquired during birth — a microbially rich and messy process that exposes the baby to a whole suite of maternal microbes. Babies born by Caesarean, however, a comparatively sterile procedure, do not acquire their mother’s vaginal and intestinal microbes at birth. Their initial gut communities more closely resemble that of their mother’s (and father’s) skin, which is less than ideal and may account for higher rates of allergy, asthma and autoimmune problems in C-section babies: not having been seeded with the optimal assortment of microbes at birth, their immune systems may fail to develop properly.

At dinner, Knight told me that he was sufficiently concerned about such an eventuality that, when his daughter was born by emergency C-section, he and his wife took matters into their own hands: using a sterile cotton swab, they inoculated the newborn infant’s skin with the mother’s vaginal secretions to insure a proper colonization. A formal trial of such a procedure is under way in Puerto Rico.

While I was in Boulder, I sat down with Catherine A. Lozupone, a microbiologist who had just left Knight’s lab to set up her own at the University of Colorado, Denver, and who spent some time looking at my microbiome and comparing it with others, including her own. Lozupone was the lead author on an important 2012 paper in Nature, “Diversity, Stability and Resilience of the Human Gut Microbiota,” which sought to approach the gut community as an ecologist might, trying to determine the “normal” state of the ecosystem and then examining the various factors that disturb it over time. How does diet affect it? Antibiotics? Pathogens? What about cultural traditions? So far, the best way to begin answering such questions may be by comparing the gut communities of various far-flung populations, and researchers have been busy collecting samples around the world and shipping them to sequencing centers for analysis. The American Gut project, which hopes to eventually sequence the communities of tens of thousands of Americans, represents the most ambitious such effort to date; it will help researchers uncover patterns of correlation between people’s lifestyle, diet, health status and the makeup of their microbial community.

It is still early days in this research, as Lozupone (and everyone else I interviewed) underscored; scientists can’t even yet say with confidence exactly what a “healthy” microbiome should look like. But some broad, intriguing patterns are emerging. More diversity is probably better than less, because a diverse ecosystem is generally more resilient — and diversity in the Western gut is significantly lower than in other, less-industrialized populations. The gut microbiota of people in the West looks very different from that of a variety of other geographically dispersed peoples. So, for example, the gut community of rural people in West Africa more closely resembles that of Amerindians in Venezuela than it does an American’s or a European’s.

These rural populations not only harbor a greater diversity of microbes but also a different cast of lead characters. American and European guts contain relatively high levels of bacteroides and firmicutes and low levels of the prevotella that dominate the guts of rural Africans and Amerindians. (It is not clear whether high or low levels of any of these is good or bad.) Why are the microbes different? It could be the diet, which in both rural populations features a considerable amount of whole grains (which prevotella appear to like), plant fiber and very little meat. (Many firmicutes like amino acids, so they proliferate when the diet contains lots of protein; bacteroides metabolize carbohydrates.) As for the lower biodiversity in the West, this could be a result of our profligate use of antibiotics (in health care as well as the food system), our diet of processed food (which has generally been cleansed of all bacteria, the good and the bad), environmental toxins and generally less “microbial pressure” — i.e., exposure to bacteria — in everyday life. All of this may help explain why, though these rural populations tend to have greater exposures to infectious diseases and lower life expectancies than those in the West, they also have lower rates of chronic disorders like allergies, asthma, Type 2 diabetes and cardiovascular disease.

“Rural people spend a lot more time outside and have much more contact with plants and with soil,” Lozupone says. Another researcher, who has gathered samples in Malawi, told me, “In some of these cultures, children are raised communally, passed from one set of hands to another, so they’re routinely exposed to a greater diversity of microbes.” The nuclear family may not be conducive to the health of the microbiome.

As it happens, Lozupone and I had something in common, microbially speaking: we share unusually high levels of prevotella for Americans. Our gut communities look more like those of rural Africans or Amerindians than like those of our neighbors. Lozupone suspects that the reasons for this might have to do with a plant-based diet; we each eat lots of whole grains and vegetables and relatively little meat. (Though neither of us is a vegetarian.) Like me, she was proud of her prevotella, regarding it as a sign of a healthy non-Western diet, at least until she began doing research on the microbiota of H.I.V. patients. It seems that they, too, have lots of prevotella. Further confusing the story, a recent study linking certain gut microbes common in meat eaters to high levels of a blood marker for heart disease suggested that prevotella was one such microbe. Early days, indeed.

Two other features of my microbiome attracted the attention of the researchers who examined it. First, the overall biodiversity of my gut community was significantly higher than that of the typical Westerner, which I decided to take as a compliment, though the extravagantly diverse community of microbes on my skin raised some eyebrows. “Where have your hands been, man?” Jeff Leach of the American Gut project asked after looking over my results. My skin harbors bacteria associated with plants, soil and a somewhat alarming variety of animal guts. I put this down to gardening, composting (I keep worms too) and also the fact that I was fermenting kimchi and making raw-milk cheese, “live-culture” foods teeming with microbes.

Compared to a rain forest or a prairie, the interior ecosystem is not well understood, but the core principles of ecology — which along with powerful new sequencing machines have opened this invisible frontier to science — are beginning to yield some preliminary answers and a great many more intriguing hypotheses. Your microbial community seems to stabilize by age 3, by which time most of the various niches in the gut ecosystem are occupied. That doesn’t mean it can’t change after that; it can, but not as readily. A change of diet or a course of antibiotics, for example, may bring shifts in the relative population of the various resident species, helping some kinds of bacteria to thrive and others to languish. Can new species be introduced? Yes, but probably only when a niche is opened after a significant disturbance, like an antibiotic storm. Just like any other mature ecosystem, the one in our gut tends to resist invasion by newcomers.

You acquire most of the initial microbes in your gut community from your parents, but others are picked up from the environment. “The world is covered in a fine patina of feces,” as the Stanford microbiologist Stanley Falkow tells students. The new sequencing tools have confirmed his hunch: Did you know that house dust can contain significant amounts of fecal particles? Or that, whenever a toilet is flushed, some of its contents are aerosolized? Knight’s lab has sequenced the bacteria on toothbrushes. This news came during breakfast, so I didn’t ask for details, but got them anyway: “You want to keep your toothbrush a minimum of six feet away from a toilet,” one of Knight’s colleagues told me.

Some scientists in the field borrow the term “ecosystem services” from ecology to catalog all the things that the microbial community does for us as its host or habitat, and the services rendered are remarkably varied and impressive. “Invasion resistance” is one. Our resident microbes work to keep pathogens from gaining a toehold by occupying potential niches or otherwise rendering the environment inhospitable to foreigners. The robustness of an individual’s gut community might explain why some people fall victim to food poisoning while others can blithely eat the same meal with no ill effects.

Our gut bacteria also play a role in the manufacture of substances like neurotransmitters (including serotonin); enzymes and vitamins (notably Bs and K) and other essential nutrients (including important amino acid and short-chain fatty acids); and a suite of other signaling molecules that talk to, and influence, the immune and the metabolic systems. Some of these compounds may play a role in regulating our stress levels and even temperament: when gut microbes from easygoing, adventurous mice are transplanted into the guts of anxious and timid mice, they become more adventurous. The expression “thinking with your gut” may contain a larger kernel of truth than we thought.

The gut microbes are looking after their own interests, chief among them getting enough to eat and regulating the passage of food through their environment. The bacteria themselves appear to help manage these functions by producing signaling chemicals that regulate our appetite, satiety and digestion. Much of what we’re learning about the microbiome’s role in human metabolism has come from studying “gnotobiotic mice” — mice raised in labs like Jeffrey I. Gordon’s at Washington University, in St. Louis, to be microbially sterile, or germ-free. Recently, Gordon’s lab transplanted the gut microbes of Malawian children with kwashiorkor — an acute form of malnutrition — into germ-free mice. The lab found those mice with kwashiorkor who were fed the children’s typical diet could not readily metabolize nutrients, indicating that it may take more than calories to remedy malnutrition. Repairing a patient’s disordered metabolism may require reshaping the community of species in his or her gut.

Keeping the immune system productively engaged with microbes — exposed to lots of them in our bodies, our diet and our environment — is another important ecosystem service and one that might turn out to be critical to our health. “We used to think the immune system had this fairly straightforward job,” Michael Fischbach, a biochemist at the University of California, San Francisco, says. “All bacteria were clearly ‘nonself’ so simply had to be recognized and dealt with. But the job of the immune system now appears to be far more nuanced and complex. It has to learn to consider our mutualists” — e.g., resident bacteria — “as self too. In the future we won’t even call it the immune system, but the microbial interaction system.” The absence of constructive engagement between microbes and immune system (particularly during certain windows of development) could be behind the increase in autoimmune conditions in the West.

So why haven’t we evolved our own systems to perform these most critical functions of life? Why have we outsourced all this work to a bunch of microbes? One theory is that, because microbes evolve so much faster than we do (in some cases a new generation every 20 minutes), they can respond to changes in the environment — to threats as well as opportunities — with much greater speed and agility than “we” can. Exquisitely reactive and adaptive, bacteria can swap genes and pieces of DNA among themselves. This versatility is especially handy when a new toxin or food source appears in the environment. The microbiota can swiftly come up with precisely the right gene needed to fight it — or eat it. In one recent study, researchers found that a common gut microbe in Japanese people has acquired a gene from a marine bacterium that allows the Japanese to digest seaweed, something the rest of us can’t do as well.

This plasticity serves to extend our comparatively rigid genome, giving us access to a tremendous bag of biochemical tricks we did not need to evolve ourselves. “The bacteria in your gut are continually reading the environment and responding,” says Joel Kimmons, a nutrition scientist and epidemiologist at the Centers for Disease Control and Prevention in Atlanta. “They’re a microbial mirror of the changing world. And because they can evolve so quickly, they help our bodies respond to changes in our environment.”

A handful of microbiologists have begun sounding the alarm about our civilization’s unwitting destruction of the human microbiome and its consequences. Important microbial species may have already gone extinct, before we have had a chance to learn who they are or what they do. What we think of as an interior wilderness may in fact be nothing of the kind, having long ago been reshaped by unconscious human actions. Taking the ecological metaphor further, the “Westernized microbiome” most of us now carry around is in fact an artifact of civilization, no more a wilderness today than, say, the New Jersey Meadowlands.

To obtain a clearer sense of what has been lost, María Gloria Dominguez-Bello, a Venezuelan-born microbiologist at New York University, has been traveling to remote corners of the Amazon to collect samples from hunter-gatherers who have had little previous contact with Westerners or Western medicine. “We want to see how the human microbiota looks before antibiotics, before processed food, before modern birth,” she told me. “These samples are really gold.”

Preliminary results indicate that a pristine microbiome — of people who have had little or no contact with Westerners — features much greater biodiversity, including a number of species never before sequenced, and, as mentioned, much higher levels of prevotella than is typically found in the Western gut. Dominguez-Bello says these vibrant, diverse and antibiotic-naïve microbiomes may play a role in Amerindians’ markedly lower rates of allergies, asthma, atopic disease and chronic conditions like Type 2 diabetes and cardiovascular disease.

One bacterium commonly found in the non-Western microbiome but nearly extinct in ours is a corkscrew-shaped inhabitant of the stomach by the name of Helicobacter pylori. Dominguez-Bello’s husband, Martin Blaser, a physician and microbiologist at N.Y.U., has been studying H. pylori since the mid-1980s and is convinced that it is an endangered species, the extinction of which we may someday rue. According to the “missing microbiota hypothesis,” we depend on microbes like H. pylori to regulate various metabolic and immune functions, and their disappearance is disordering those systems. The loss is cumulative: “Each generation is passing on fewer of these microbes,” Blaser told me, with the result that the Western microbiome is being progressively impoverished.

He calls H. pylori the “poster child” for the missing microbes and says medicine has actually been trying to exterminate it since 1983, when Australian scientists proposed that the microbe was responsible for peptic ulcers; it has since been implicated in stomach cancer as well. But H. pylori is a most complicated character, the entire spectrum of microbial good and evil rolled into one bug. Scientists learned that H. pylori also plays a role in regulating acid in the stomach. Presumably it does this to render its preferred habitat inhospitable to competitors, but the effect on its host can be salutary. People without H. pylori may not get peptic ulcers, but they frequently do suffer from acid reflux. Untreated, this can lead to Barrett’s esophagus and, eventually, a certain type of esophageal cancer, rates of which have soared in the West as H. pylori has gone missing.

When after a recent bout of acid reflux, my doctor ordered an endoscopy, I discovered that, like most Americans today, my stomach has no H. pylori. My gastroenterologist was pleased, but after talking to Blaser, the news seemed more equivocal, because H. pylori also does us a lot of good. The microbe engages with the immune system, quieting the inflammatory response in ways that serve its own interests — to be left in peace — as well as our own. This calming effect on the immune system may explain why populations that still harbor H. pylori are less prone to allergy and asthma. Blaser’s lab has also found evidence that H. pylori plays an important role in human metabolism by regulating levels of the appetite hormone ghrelin. “When the stomach is empty, it produces a lot of ghrelin, the chemical signal to the brain to eat,” Blaser says. “Then, when it has had enough, the stomach shuts down ghrelin production, and the host feels satiated.” He says the disappearance of H. pylori may be contributing to obesity by muting these signals.

But what about the diseases H. pylori is blamed for? Blaser says these tend to occur only late in life, and he makes the rather breathtaking suggestion that this microbe’s evolutionary role might be to help shuffle us off life’s stage once our childbearing years have passed. So important does Blaser regard this strange, paradoxical symbiont that he has proposed not one but two unconventional therapeutic interventions: inoculate children with H. pylori to give them the benefit of its services early in life, and then exterminate it with antibiotics at age 40, when it is liable to begin causing trouble.

These days Blaser is most concerned about the damage that antibiotics, even in tiny doses, are doing to the microbiome — and particularly to our immune system and weight. “Farmers have been performing a great experiment for more than 60 years,” Blaser says, “by giving subtherapeutic doses of antibiotics to their animals to make them gain weight.” Scientists aren’t sure exactly why this practice works, but the drugs may favor bacteria that are more efficient at harvesting energy from the diet. “Are we doing the same thing to our kids?” he asks. Children in the West receive, on average, between 10 and 20 courses of antibiotics before they turn 18. And those prescribed drugs aren’t the only antimicrobials finding their way to the microbiota; scientists have found antibiotic residues in meat, milk and surface water as well. Blaser is also concerned about the use of antimicrobial compounds in our diet and everyday lives — everything from chlorine washes for lettuce to hand sanitizers. “We’re using these chemicals precisely because they’re antimicrobial,” Blaser says. “And of course they do us some good. But we need to ask, what are they doing to our microbiota?” No one is questioning the value of antibiotics to civilization — they have helped us to conquer a great many infectious diseases and increased our life expectancy. But, as in any war, the war on bacteria appears to have had some unintended consequences.

One of the more striking results from the sequencing of my microbiome was the impact of a single course of antibiotics on my gut community. My dentist had put me on a course of Amoxicillin as a precaution before oral surgery. (Without prophylactic antibiotics, of course, surgery would be considerably more dangerous.) Within a week, my impressively non-Western “alpha diversity” — a measure of the microbial diversity in my gut — had plummeted and come to look very much like the American average. My (possibly) healthy levels of prevotella had also disappeared, to be replaced by a spike in bacteroides (much more common in the West) and an alarming bloom of proteobacteria, a phylum that includes a great many weedy and pathogenic characters, including E. coli and salmonella. What had appeared to be a pretty healthy, diversified gut was now raising expressions of concern among the microbiologists who looked at my data.

“Your E. coli bloom is creepy,” Ruth Ley, a Cornell University microbiologist who studies the microbiome’s role in obesity, told me. “If we put that sample in germ-free mice, I bet they’d get inflamed.” Great. Just when I was beginning to think of myself as a promising donor for a fecal transplant, now I had a gut that would make mice sick. I was relieved to learn that my gut community would eventually bounce back to something resembling its former state. Yet one recent study found that when subjects were given a second course of antibiotics, the recovery of their interior ecosystem was less complete than after the first.

Few of the scientists I interviewed had much doubt that the Western diet was altering our gut microbiome in troubling ways. Some, like Blaser, are concerned about the antimicrobials we’re ingesting with our meals; others with the sterility of processed food. Most agreed that the lack of fiber in the Western diet was deleterious to the microbiome, and still others voiced concerns about the additives in processed foods, few of which have ever been studied for their specific effects on the microbiota. According to a recent article in Nature by the Stanford microbiologist Justin Sonnenburg, “Consumption of hyperhygienic, mass-produced, highly processed and calorie-dense foods is testing how rapidly the microbiota of individuals in industrialized countries can adapt.” As our microbiome evolves to cope with the Western diet, Sonnenburg says he worries that various genes are becoming harder to find as the microbiome’s inherent biodiversity declines along with our everyday exposure to bacteria.

Catherine Lozupone in Boulder and Andrew Gewirtz, an immunologist at Georgia State University, directed my attention to the emulsifiers commonly used in many processed foods — ingredients with names like lecithin, Datem, CMC and polysorbate 80. Gewirtz’s lab has done studies in mice indicating that some of these detergentlike compounds may damage the mucosa — the protective lining of the gut wall — potentially leading to leakage and inflammation.

A growing number of medical researchers are coming around to the idea that the common denominator of many, if not most, of the chronic diseases from which we suffer today may be inflammation — a heightened and persistent immune response by the body to a real or perceived threat. Various markers for inflammation are common in people with metabolic syndrome, the complex of abnormalities that predisposes people to illnesses like cardiovascular disease, obesity, Type 2 diabetes and perhaps cancer. While health organizations differ on the exact definition of metabolic syndrome, a 2009 report from the Centers for Disease Control and Prevention found that 34 percent of American adults are afflicted with the condition. But is inflammation yet another symptom of metabolic syndrome, or is it perhaps the cause of it? And if it is the cause, what is its origin?

One theory is that the problem begins in the gut, with a disorder of the microbiota, specifically of the all-important epithelium that lines our digestive tract. This internal skin — the surface area of which is large enough to cover a tennis court — mediates our relationship to the world outside our bodies; more than 50 tons of food pass through it in a lifetime. The microbiota play a critical role in maintaining the health of the epithelium: some bacteria, like the bifidobacteria and Lactobacillus plantarum (common in fermented vegetables), seem to directly enhance its function. These and other gut bacteria also contribute to its welfare by feeding it. Unlike most tissues, which take their nourishment from the bloodstream, epithelial cells in the colon obtain much of theirs from the short-chain fatty acids that gut bacteria produce as a byproduct of their fermentation of plant fiber in the large intestine.

But if the epithelial barrier isn’t properly nourished, it can become more permeable, allowing it to be breached. Bacteria, endotoxins — which are the toxic byproducts of certain bacteria — and proteins can slip into the blood stream, thereby causing the body’s immune system to mount a response. This resulting low-grade inflammation, which affects the entire body, may lead over time to metabolic syndrome and a number of the chronic diseases that have been linked to it.

Evidence in support of this theory is beginning to accumulate, some of the most intriguing coming from the lab of Patrice Cani at the Université Catholique de Louvain in Brussels. When Cani fed a high-fat, “junk food” diet to mice, the community of microbes in their guts changed much as it does in humans on a fast-food diet. But Cani also found the junk-food diet made the animals’ gut barriers notably more permeable, allowing endotoxins to leak into the bloodstream. This produced a low-grade inflammation that eventually led to metabolic syndrome. Cani concludes that, at least in mice, “gut bacteria can initiate the inflammatory processes associated with obesity and insulin resistance” by increasing gut permeability.

These and other experiments suggest that inflammation in the gut may be the cause of metabolic syndrome, not its result, and that changes in the microbial community and lining of the gut wall may produce this inflammation. If Cani is correct — and there is now some evidence indicating that the same mechanism is at work in humans — then medical science may be on the trail of a Grand Unified Theory of Chronic Disease, at the very heart of which we will find the gut microbiome.

My first reaction to learning all this was to want to do something about it immediately, something to nurture the health of my microbiome. But most of the scientists I interviewed were reluctant to make practical recommendations; it’s too soon, they told me, we don’t know enough yet. Some of this hesitance reflects an understandable abundance of caution. The microbiome researchers don’t want to make the mistake of overpromising, as the genome researchers did. They are also concerned about feeding a gigantic bloom of prebiotic and probiotic quackery and rightly so: probiotics are already being hyped as the new panacea, even though it isn’t at all clear what these supposedly beneficial bacteria do for us or how they do what they do. There is some research suggesting that some probiotics may be effective in a number of ways: modulating the immune system; reducing allergic response; shortening the length and severity of colds in children; relieving diarrhea and irritable bowel symptoms; and improving the function of the epithelium. The problem is that, because the probiotic marketplace is largely unregulated, it’s impossible to know what, if anything, you’re getting when you buy a “probiotic” product. One study tested 14 commercial probiotics and found that only one contained the exact species stated on the label.

But some of the scientists’ reluctance to make recommendations surely flows from the institutional bias of science and medicine: that the future of microbiome management should remain firmly in the hands of science and medicine. Down this path — which holds real promise — lie improved probiotics and prebiotics, fecal transplants (with better names) and related therapies. Jeffrey Gordon, one of those scientists who peers far over the horizon, looks forward to a time when disorders of the microbiome will be treated with “synbiotics” — suites of targeted, next-generation probiotic microbes administered along with the appropriate prebiotic nutrients to nourish them. The fecal transplant will give way to something far more targeted: a purified and cultured assemblage of a dozen or so microbial species that, along with new therapeutic foods, will be introduced to the gut community to repair “lesions” — important missing species or functions. Yet, assuming it all works as advertised, such an approach will also allow Big Pharma and Big Food to stake out and colonize the human microbiome for profit.

When I asked Gordon about do-it-yourself microbiome management, he said he looked forward to a day “when people can cultivate this wonderful garden that is so influential in our health and well-being” — but that day awaits a lot more science. So he declined to offer any gardening tips or dietary advice. “We have to manage expectations,” he said.

Alas, I am impatient. So I gave up asking scientists for recommendations and began asking them instead how, in light of what they’ve learned about the microbiome, they have changed their own diets and lifestyles. Most of them have made changes. They were slower to take, or give their children, antibiotics. (I should emphasize that in no way is this an argument for the rejection of antibiotics when they are medically called for.) Some spoke of relaxing the sanitary regime in their homes, encouraging their children to play outside in the dirt and with animals — deliberately increasing their exposure to the great patina. Many researchers told me they had eliminated or cut back on processed foods, either because of its lack of fiber or out of concern about additives. In general they seemed to place less faith in probiotics (which few of them used) than in prebiotics — foods likely to encourage the growth of “good bacteria” already present. Several, including Justin Sonnenburg, said they had added fermented foods to their diet: yogurt, kimchi, sauerkraut. These foods can contain large numbers of probiotic bacteria, like L. plantarum and bifidobacteria, and while most probiotic bacteria don’t appear to take up permanent residence in the gut, there is evidence that they might leave their mark on the community, sometimes by changing the gene expression of the permanent residents — in effect turning on or off metabolic pathways within the cell — and sometimes by stimulating or calming the immune response.

What about increasing our exposure to bacteria? “There’s a case for dirtying up your diet,” Sonnenburg told me. Yet advising people not to thoroughly wash their produce is probably unwise in a world of pesticide residues. “I view it as a cost-benefit analysis,” Sonnenburg wrote in an e-mail. “Increased exposure to environmental microbes likely decreases chance of many Western diseases, but increases pathogen exposure. Certainly the costs go up as scary antibiotic-resistant bacteria become more prevalent.” So wash your hands in situations when pathogens or toxic chemicals are likely present, but maybe not after petting your dog. “In terms of food, I think eating fermented foods is the answer — as opposed to not washing food, unless it is from your garden,” he said.

With his wife, Erica, also a microbiologist, Sonnenburg tends a colony of gnotobiotic mice at Stanford, examining (among other things) the effects of the Western diet on their microbiota. (Removing fiber drives down diversity, but the effect is reversible.) He’s an amateur baker, and when I visited his lab, we talked about the benefits of baking with whole grains.

“Fiber is not a single nutrient,” Sonnenburg said, which is why fiber supplements are no magic bullet. “There are hundreds of different polysaccharides” — complex carbohydrates, including fiber — “in plants, and different microbes like to chomp on different ones.” To boost fiber, the food industry added lots of a polysaccharide called inulin to hundreds of products, but that’s just one kind (often derived from the chicory-plant root) and so may only favor a limited number of microbes. I was hearing instead an argument for a variety of whole grains and a diverse diet of plants and vegetables as well as fruits. “The safest way to increase your microbial biodiversity is to eat a variety of polysaccharides,” he said.

His comment chimed with something a gastroenterologist at the University of Pittsburgh told me. “The big problem with the Western diet,” Stephen O’Keefe said, “is that it doesn’t feed the gut, only the upper G I. All the food has been processed to be readily absorbed, leaving nothing for the lower G I. But it turns out that one of the keys to health is fermentation in the large intestine.” And the key to feeding the fermentation in the large intestine is giving it lots of plants with their various types of fiber, including resistant starch (found in bananas, oats, beans); soluble fiber (in onions and other root vegetables, nuts); and insoluble fiber (in whole grains, especially bran, and avocados).

With our diet of swiftly absorbed sugars and fats, we’re eating for one and depriving the trillion of the food they like best: complex carbohydrates and fermentable plant fibers. The byproduct of fermentation is the short-chain fatty acids that nourish the gut barrier and help prevent inflammation. And there are studies suggesting that simply adding plants to a fast-food diet will mitigate its inflammatory effect.

The outlines of a diet for the new superorganism were coming clear, and it didn’t require the ministrations of the food scientists at Nestlé or General Mills to design it. Big Food and Big Pharma probably do have a role to play, as will Jeffrey Gordon’s next-generation synbiotics, in repairing the microbiota of people who can’t or don’t care to simply change their diets. This is going to be big business. Yet the components of a microbiota-friendly diet are already on the supermarket shelves and in farmers’ markets.

Viewed from this perspective, the foods in the markets appear in a new light, and I began to see how you might begin to shop and cook with the microbiome in mind, the better to feed the fermentation in our guts. The less a food is processed, the more of it that gets safely through the gastrointestinal tract and into the eager clutches of the microbiota. Al dente pasta, for example, feeds the bugs better than soft pasta does; steel-cut oats better than rolled; raw or lightly cooked vegetables offer the bugs more to chomp on than overcooked, etc. This is at once a very old and a very new way of thinking about food: it suggests that all calories are not created equal and that the structure of a food and how it is prepared may matter as much as its nutrient composition.

It is a striking idea that one of the keys to good health may turn out to involve managing our internal fermentation. Having recently learned to manage several external fermentations — of bread and kimchi and beer — I know a little about the vagaries of that process. You depend on the microbes, and you do your best to align their interests with yours, mainly by feeding them the kinds of things they like to eat — good “substrate.” But absolute control of the process is too much to hope for. It’s a lot more like gardening than governing.

The successful gardener has always known you don’t need to master the science of the soil, which is yet another hotbed of microbial fermentation, in order to nourish and nurture it. You just need to know what it likes to eat — basically, organic matter — and how, in a general way, to align your interests with the interests of the microbes and the plants. The gardener also discovers that, when pathogens or pests appear, chemical interventions “work,” that is, solve the immediate problem, but at a cost to the long-term health of the soil and the whole garden. The drive for absolute control leads to unanticipated forms of disorder.

This, it seems to me, is pretty much where we stand today with respect to our microbiomes — our teeming, quasi-wilderness. We don’t know a lot, but we probably know enough to begin taking better care of it. We have a pretty good idea of what it likes to eat, and what strong chemicals do to it. We know all we need to know, in other words, to begin, with modesty, to tend the unruly garden within.

I don't know, maybe it's just me....

Fri, 17 May 2013 17:39:28 GMT

But is it that unreasonable to expect that the target audience of a book about a sixth grader would already KNOW Santa doesn't exist? And also that babies do not, in fact, come from the stork?

(Also, when people start pulling out words like "reprehensible" to describe Superfudge, is it wrong of me to give up and point out that you surely KNEW this would be the eventual outcome of telling your kids about Santa and its hardly Judy Blume's fault that this is the bed you made? I mean, honestly, how do people think it's going to work that year when their kids find out?)

Also...

Fri, 17 May 2013 13:07:30 GMT

http://chicshorties.tumblr.com/post/50649439331/anna-age-10-wears-wigs-as-often-as-she-can-get

Enjoy! She really does wear wigs all the time. (It's just a pity the wig covers up her new short hairstyle.)

Ana is ten now!

Fri, 17 May 2013 13:05:07 GMT

And since the 15th fell on a Wednesday we ditched school and went to the Bronx Zoo, which is free Wednesdays. I say free, but we bought the discounted Total Experience tickets anyway, and then the girls didn't end up wanting to see/do even one of the special exhibits! Sheesh.

To make things worse, it turns out that being a camel is a union job, and they won't work in the rain. Three times we've gone there, three times we've utterly failed to get a camel ride. But we did get to see a crane come very very close to us, and see the tigers, and generally enjoy our visit, so that's all right. We finished the day with a visit to the playground and two different bookstores, and then went out to a restaurant which had THE COOLEST HAND DRIERS EVER. Eva's face as she used it was hilarious. Ana didn't need help figuring out the sink fixtures, so I don't know how her face looked.

And now Ana is ten! Double digits! I am... so not ready for this. I'm trying to let it sink in gradually.

I'm rereading The Phoenix and the Carpet right now.

Fri, 17 May 2013 02:53:36 GMT

Sometimes it's nice to do that, re-read a classic you haven't read in ages. Especially when it's Nesbit. Reading about what she apparently considered perfectly normal behavior for kids is incredibly reassuring. More authors, past and present, could stand to copy her ideas here!

Two freebies!

Fri, 17 May 2013 01:14:55 GMT

Times subscription given away!

Secondly, free in a box of Parcheesi, of all things, a year's subscription to Family Circle. If you've never had the pleasure, Family Circle is, in their words, "filled with quick and easy recipes, do it yourself decorating, fat fighting secrets, family advice, great ideas for getting organized, and more." Except they don't use the Oxford comma. Those bastards! If you have kids at home, or teach art at school, Family Circle is one of those magazines that is great for cutting pictures out of. At least, it was when I was a kid. If you want the subscription, post your address, and it'll go to the first poster. Comments are screened, of course.

The things people dream up...!

Tue, 14 May 2013 16:45:48 GMT

Apparently, it is possible now to rent a chicken.

http://www.landssake.org/farm/rent-a-chicken

Of all the silly things....

I'm not a fan of the snooze alarm.

Sun, 12 May 2013 00:29:07 GMT

It occurs to me that trading thirty minutes of sleep for thirty minutes of disrupted sleep is a pretty bad exchange. And who are you kidding? If you set your alarm 30 minutes early, but you don't really *need* to get up at that time, do you honestly expect you'll get up half an hour earlier than you actually need to?

I went and googled about this, and it turns out that the snooze alarm is even worse than I thought. At least, according to Google. Apparently, it sends you back into deep sleep, and what's the point of that? Ever since I worked this out, I've lived by the simple rule: set the clock when you're willing to get up, then get up. If you realize you set it an hour too early, cut your losses and reset it then and there for a new time, don't do that silly snooze thing.

Wow.

Sat, 11 May 2013 22:06:46 GMT

Meet the Family That Never Learned to Walk on Two Legs

You can see the cited video on YouTube.

Choco pies: The smuggled treats of North Korea

Fri, 10 May 2013 17:02:42 GMT

http://www.bbc.co.uk/news/magazine-22383586

Another kid has been documenting his school lunches

Fri, 10 May 2013 16:25:41 GMT

http://cityroom.blogs.nytimes.com/2013/05/09/the-michael-moore-of-the-grade-school-lunchroom

They're very... brown.

The comments are full of people complaining that lawyers are all rich and thus ever entitled to free lunch. I would think that a career that takes three years off of your working life and costs an additional $100,000 on top of college before you even get started doesn't actually guarantee instant wealth (and we don't even know what kind of lawer the kid's dad is), but apparently it is supposed to. At any rate, to save money the city made all school lunches free after the hurricane, so whatever.

This is going to keep me up all night

Thu, 09 May 2013 00:08:48 GMT

What is the plural of Spider-Man (and likewise Batman and Superman)?

Why is it that when I try to find new recipes for beans I keep finding the old ones?

Wed, 08 May 2013 17:49:10 GMT

Kidney beans in chili. White beans with greens and sausage. Split pea soup. Black beans with cilantro or sweet potato or both. Chickpeas for hummus. Nothing wrong with any of those, but isn't there more to life? And nobody is such a fan of soup here anyway.

I could crack open my Indian cookbook, which has a plethora of bean recipes, and lentils, but much though I adore it I don't want to eat from it every day.

In other, more cheerful news, George Takei continues to be awesome.

Wed, 08 May 2013 13:51:36 GMT

http://www.funnyordie.com/videos/34201d7411/gay-beware-with-jesse-tyler-ferguson

And here is an article about Ancient Greek statues and how they were painted:

http://gizmodo.com/5616498/ultraviolet-light-reveals-how-ancient-greek-statues-really-looked

Apparently, some of the neighbors had called the cops before

Wed, 08 May 2013 13:47:59 GMT

But nothing ever came of it. Some of the information in the articles is pretty upsetting, so read at your own risk:

http://www.usatoday.com/story/news/nation/2013/05/07/missing-women-cleveland-brothers-arrested/2140359/

http://www.nytimes.com/2013/05/08/us/cleveland-kidnapping.html

Wow.

Tue, 07 May 2013 02:47:20 GMT

Three women, missing for a decade or more each, were found today, alive and physically well.

http://www.cleveland.com/metro/index.ssf/2013/05/tv_station_reports_berry_dejes.html

That is the ending only the most devoted expected, I'm sure.

OMG OMG OMG!!!!!!!

Mon, 06 May 2013 17:32:16 GMT

If you've always wanted to run a streetcar or subway train, take advantage of this opportunity at the Shore Line Trolley Museum by signing up for the Guest Operator program.
You'll be given an overview of operating principles by one of our instructors. Then it will be your turn to take the handles and operate solo! Don't worry, you won't have any regular passengers, just you, your instructor, and your invited guests.

http://www.bera.org/guestop.html

I know what I'm doing some time this summer!

Put all seedlings in the dirt.

Sat, 04 May 2013 21:34:49 GMT

Tomatoes, peppers, and watermelon. Hardly any of the watermelon germinated, and not all the peppers and tomatoes did. If I go with seeds next year I definitely won't skimp on the starting pots again. Egg cartons are free, but they dry out faster.

I might not go with seeds, though, might just order plants. Starting seeds indoors, they need space, they need to be kept moist but not TOO moist, warm but not TOO warm, I have to keep the cats away, I have to harden them off before transplant, and don't forget having to thin them! (It always makes me feel like a particularly callous murderer.) The whole enterprise is like having extra children around.

As you no doubt guessed, I'm clearing out some articles.

Sat, 04 May 2013 15:13:23 GMT

A Haven for the Deaf Draws Federal Scrutiny Over Potential Discrimination

http://nyti.ms/10mcy0Z

TEMPE, Ariz. — When the subsidized housing complex for senior citizens opened its doors here last year, it already had a waiting list. Designed by a deaf architect to fit the needs of the deaf, its units have video phones and lights that flash when the phone or the doorbell rings. Wiring in common areas pipes announcements made through loudspeakers into residents’ hearing aids.

The complex, meant to foster a sense of community among residents who use sign language to communicate and socialize, was the first of its kind in the Southwest. For the Arizona Department of Housing, which allocated federal money to help pay for it, it was a milestone, one that advocates for the disabled hoped would be a model for similar projects.

Preference was given to deaf and hard-of-hearing applicants, who occupy 69 of the complex’s 75 units. The arrangement seemed to make sense; the state and the project’s developer were convinced that they stood on solid legal ground.

But after an audit last year, the federal Department of Housing and Urban Development began raising questions.

The project, named Apache ASL Trails in a reference to American Sign Language, now finds itself in an unlikely spot, facing charges of discrimination for favoring deaf and hard-of-hearing people over others, disabled or not. The federal agency released its finding in January after examining marketing materials and the project’s criteria for tenant selection, even though the developer assured it that the documents in question had been misinterpreted or were outdated.

Last June, HUD drafted a compliance agreement limiting the number of units set aside for deaf residents, which seems to have only stoked the dispute. State officials said the agency at one point threatened to withhold money from the state if it did not continue with the plan. But the state housing director, Michael Trailor, did not back down, saying he had to “stand up for the rights of disabled people.”

Advocates for the disabled fear that the finding might complicate other projects in which federal money would be used to build housing for adults with special needs. Already, the Southwest Autism Research and Resource Center, based in Phoenix, has scrapped plans to use federal grants to help pay for a development designed for autistic adults, opting instead to pursue private financing.

Through combative legal correspondence and in emotional meetings, the parties in the Tempe project, working to negotiate a compromise, have argued over the meaning of the federal statute governing fair housing practices and the word “discrimination” as it applies to the deaf.

John Trasviña, HUD’s assistant secretary for fair housing and equal opportunity, said in a statement that “federal law prohibits facilities that receive HUD funds from providing separate or different housing for one group of individuals with disabilities because this practice denies or limits access to housing for other individuals based on the types of disabilities they have.” (The agency did not make Mr. Trasviña or other officials available for on-the-record interviews.)

In interviews, Mr. Trailor and the developer, Erich Schwenker of Cardinal Capital Management, which is based in Milwaukee, said the units were advertised in publications that focused on the deaf population, but also in the state’s largest newspaper and in a local magazine.

“Our intention has never been to exclude, but to make sure the units are utilized to the fullest extent possible, as the law requires,” Mr. Schwenker said.

The demands from HUD mobilized advocacy groups across the country. Last week, 75 of them signed a letter from the National Association of the Deaf to the federal housing secretary, Shaun Donovan, accusing HUD of “forcing deaf and hard-of-hearing individuals to only live according to an ideological vision of forced integration.”

In an interview, the association’s chief executive officer, Howard Rosenblum, said the approach “ignores the unique communication needs” of the deaf, making them more isolated. Denise Resnik, a co-founder of the Southwest autism center, said the agency’s attitude felt “like reverse discrimination.”

By Friday, HUD had scaled back its efforts. A spokesman said the agency had decided to “take a pause” in the negotiations to give the state and the developer time to submit evidence demonstrating the housing needs of the deaf population to justify the use of federal money in the project.

Jeff Rosen, the chairman of the National Council on Disability, which advises the federal government on disability policy, said these types of discussions could help the government better understand the challenges faced by groups of disabled people like the deaf, who do not often have the opportunity to live in a community that they feel is “appropriate and fit for them.” (The council has not taken an official position on the Apache ASL Trails case.)

“Our understanding of discrimination and disability policies is evolving,” Mr. Rosen, who is deaf, said through a sign-language interpreter.

“In the past, our interest was really more focused on providing basic access to opportunities,” he said. “Now, we’re having a more involved conversation that includes living the way we choose. That’s the type of evolution we’re talking about, and it is not unique to deaf people.”

A report by the National Fair Housing Alliance last year ranked disability as by far the main source of housing discrimination complaints received by HUD, representing 54.9 percent of them in 2011.

There have been no formal complaints filed against Apache ASL Trails, federal officials acknowledged. The agency learned of the potential irregularities during an audit last year of Arizona’s use of HOME grants, which are given to state and local governments to create affordable housing for low-income families. It is the state’s responsibility to ensure that the grants comply with federal law.

Agency officials said that other housing developments offering accommodations for the deaf had been partly paid for with HUD grants, but gave no overwhelming preference to deaf tenants or did not exclude other groups in their advertising.

Tanya Towers in Manhattan is the only complex among the handful of examples given by HUD that currently houses only deaf and hard-of-hearing people, although others can apply, federal officials said.

Mr. Trasviña said no one living at Apache ASL Trails would be displaced. The compliance agreement with HUD would limit the number of units set aside for tenants who are hearing-impaired or in wheelchairs to roughly 19, or 25 percent of its 75 units.

The dispute over the agreement has consumed many hours for lawyers on both sides. Mr. Schwenker, the developer, said the agency cobbled together sections of a Web site for a group of hearing-impaired senior citizens to justify its claim that marketing for the units was exclusionary. Agency officials did not disclose which promotional materials they specifically took issue with, citing the continuing negotiations.

Apache ASL Trails was built near the light-rail line that links Tempe to Phoenix and Mesa. Its resident manager, Linda Russell, is deaf; through an interpreter, she said she communicated with residents who do not know sign language through notes scribbled on paper or on the white board she keeps in her office.

A nonprofit organization offering sign-language interpretation and other services has an office in the complex. Weekly workshops — both spoken and with simultaneous sign-language translation — are held in its lobby.

“A lot of the people who live here, we share common language; we’re able to socialize,” Mary Susan Case, 72, who was born deaf to a hearing family, said through an interpreter. “I’m not lonely anymore.”

No Rich Child Left Behind

http://nyti.ms/184oVX2

Here’s a fact that may not surprise you: the children of the rich perform better in school, on average, than children from middle-class or poor families. Students growing up in richer families have better grades and higher standardized test scores, on average, than poorer students; they also have higher rates of participation in extracurricular activities and school leadership positions, higher graduation rates and higher rates of college enrollment and completion.

Whether you think it deeply unjust, lamentable but inevitable, or obvious and unproblematic, this is hardly news. It is true in most societies and has been true in the United States for at least as long as we have thought to ask the question and had sufficient data to verify the answer.

What is news is that in the United States over the last few decades these differences in educational success between high- and lower-income students have grown substantially.

One way to see this is to look at the scores of rich and poor students on standardized math and reading tests over the last 50 years. When I did this using information from a dozen large national studies conducted between 1960 and 2010, I found that the rich-poor gap in test scores is about 40 percent larger now than it was 30 years ago.

To make this trend concrete, consider two children, one from a family with income of $165,000 and one from a family with income of $15,000. These incomes are at the 90th and 10th percentiles of the income distribution nationally, meaning that 10 percent of children today grow up in families with incomes below $15,000 and 10 percent grow up in families with incomes above $165,000.

In the 1980s, on an 800-point SAT-type test scale, the average difference in test scores between two such children would have been about 90 points; today it is 125 points. This is almost twice as large as the 70-point test score gap between white and black children. Family income is now a better predictor of children’s success in school than race.

The same pattern is evident in other, more tangible, measures of educational success, like college completion. In a study similar to mine, Martha J. Bailey and Susan M. Dynarski, economists at the University of Michigan, found that the proportion of students from upper-income families who earn a bachelor’s degree has increased by 18 percentage points over a 20-year period, while the completion rate of poor students has grown by only 4 points.

In a more recent study, my graduate students and I found that 15 percent of high-income students from the high school class of 2004 enrolled in a highly selective college or university, while fewer than 5 percent of middle-income and 2 percent of low-income students did.

These widening disparities are not confined to academic outcomes: new research by the Harvard political scientist Robert D. Putnam and his colleagues shows that the rich-poor gaps in student participation in sports, extracurricular activities, volunteer work and church attendance have grown sharply as well.

In San Francisco this week, more than 14,000 educators and education scholars have gathered for the annual meeting of the American Educational Research Association. The theme this year is familiar: Can schools provide children a way out of poverty?

We are still talking about this despite decades of clucking about the crisis in American education and wave after wave of school reform.Whatever we’ve been doing in our schools, it hasn’t reduced educational inequality between children from upper- and lower-income families.

Part of knowing what we should do about this is understanding how and why these educational disparities are growing. For the past few years, alongside other scholars, I have been digging into historical data to understand just that. The results of this research don’t always match received wisdom or playground folklore.

The most potent development over the past three decades is that the test scores of children from high-income families have increased very rapidly. Before 1980, affluent students had little advantage over middle-class students in academic performance; most of the socioeconomic disparity in academics was between the middle class and the poor. But the rich now outperform the middle class by as much as the middle class outperform the poor. Just as the incomes of the affluent have grown much more rapidly than those of the middle class over the last few decades, so, too, have most of the gains in educational success accrued to the children of the rich.

Before we can figure out what’s happening here, let’s dispel a few myths.

The income gap in academic achievement is not growing because the test scores of poor students are dropping or because our schools are in decline. In fact, average test scores on the National Assessment of Educational Progress, the so-called Nation’s Report Card, have been rising — substantially in math and very slowly in reading — since the 1970s. The average 9-year-old today has math skills equal to those her parents had at age 11, a two-year improvement in a single generation. The gains are not as large in reading and they are not as large for older students, but there is no evidence that average test scores have declined over the last three decades for any age or economic group.

The widening income disparity in academic achievement is not a result of widening racial gaps in achievement, either. The achievement gaps between blacks and whites, and Hispanic and non-Hispanic whites have been narrowing slowly over the last two decades, trends that actually keep the yawning gap between higher- and lower-income students from getting even wider. If we look at the test scores of white students only, we find the same growing gap between high- and low-income children as we see in the population as a whole.

It may seem counterintuitive, but schools don’t seem to produce much of the disparity in test scores between high- and low-income students. We know this because children from rich and poor families score very differently on school readiness tests when they enter kindergarten, and this gap grows by less than 10 percent between kindergarten and high school. There is some evidence that achievement gaps between high- and low-income students actually narrow during the nine-month school year, but they widen again in the summer months.

That isn’t to say that there aren’t important differences in quality between schools serving low- and high-income students — there certainly are — but they appear to do less to reinforce the trends than conventional wisdom would have us believe.

If not the usual suspects, what’s going on? It boils down to this: The academic gap is widening because rich students are increasingly entering kindergarten much better prepared to succeed in school than middle-class students. This difference in preparation persists through elementary and high school.

My research suggests that one part of the explanation for this is rising income inequality. As you may have heard, the incomes of the rich have grown faster over the last 30 years than the incomes of the middle class and the poor. Money helps families provide cognitively stimulating experiences for their young children because it provides more stable home environments, more time for parents to read to their children, access to higher-quality child care and preschool and — in places like New York City, where 4-year-old children take tests to determine entry into gifted and talented programs — access to preschool test preparation tutors or the time to serve as tutors themselves.

But rising income inequality explains, at best, half of the increase in the rich-poor academic achievement gap. It’s not just that the rich have more money than they used to, it’s that they are using it differently. This is where things get really interesting.

High-income families are increasingly focusing their resources — their money, time and knowledge of what it takes to be successful in school — on their children’s cognitive development and educational success. They are doing this because educational success is much more important than it used to be, even for the rich.

With a college degree insufficient to ensure a high-income job, or even a job as a barista, parents are now investing more time and money in their children’s cognitive development from the earliest ages. It may seem self-evident that parents with more resources are able to invest more — more of both money and of what Mr. Putnam calls “‘Goodnight Moon’ time” — in their children’s development. But even though middle-class and poor families are also increasing the time and money they invest in their children, they are not doing so as quickly or as deeply as the rich.

The economists Richard J. Murnane and Greg J. Duncan report that from 1972 to 2006 high-income families increased the amount they spent on enrichment activities for their children by 150 percent, while the spending of low-income families grew by 57 percent over the same time period. Likewise, the amount of time parents spend with their children has grown twice as fast since 1975 among college-educated parents as it has among less-educated parents. The economists Garey Ramey and Valerie A. Ramey of the University of California, San Diego, call this escalation of early childhood investment “the rug rat race,” a phrase that nicely captures the growing perception that early childhood experiences are central to winning a lifelong educational and economic competition.

It’s not clear what we should do about all this. Partly that’s because much of our public conversation about education is focused on the wrong culprits: we blame failing schools and the behavior of the poor for trends that are really the result of deepening income inequality and the behavior of the rich.

We’re also slow to understand what’s happening, I think, because the nature of the problem — a growing educational gap between the rich and the middle class — is unfamiliar. After all, for much of the last 50 years our national conversation about educational inequality has focused almost exclusively on strategies for reducing inequalities between the educational successes of the poor and the middle class, and it has relied on programs aimed at the poor, like Head Start and Title I.

We’ve barely given a thought to what the rich were doing. With the exception of our continuing discussion about whether the rising costs of higher education are pricing the middle class out of college, we don’t have much practice talking about what economists call “upper-tail inequality” in education, much less success at reducing it.

Meanwhile, not only are the children of the rich doing better in school than even the children of the middle class, but the changing economy means that school success is increasingly necessary to future economic success, a worrisome mutual reinforcement of trends that is making our society more socially and economically immobile.

We need to start talking about this. Strangely, the rapid growth in the rich-poor educational gap provides a ray of hope: if the relationship between family income and educational success can change this rapidly, then it is not an immutable, inevitable pattern. What changed once can change again. Policy choices matter more than we have recently been taught to think.

So how can we move toward a society in which educational success is not so strongly linked to family background? Maybe we should take a lesson from the rich and invest much more heavily as a society in our children’s educational opportunities from the day they are born. Investments in early-childhood education pay very high societal dividends. That means investing in developing high-quality child care and preschool that is available to poor and middle-class children. It also means recruiting and training a cadre of skilled preschool teachers and child care providers. These are not new ideas, but we have to stop talking about how expensive and difficult they are to implement and just get on with it.

But we need to do much more than expand and improve preschool and child care. There is a lot of discussion these days about investing in teachers and “improving teacher quality,” but improving the quality of our parenting and of our children’s earliest environments may be even more important. Let’s invest in parents so they can better invest in their children.

This means finding ways of helping parents become better teachers themselves. This might include strategies to support working families so that they can read to their children more often.. It also means expanding programs like the Nurse-Family Partnership that have proved to be effective at helping single parents educate their children; but we also need to pay for research to develop new resources for single parents.

It might also mean greater business and government support for maternity and paternity leave and day care so that the middle class and the poor can get some of the educational benefits that the early academic intervention of the rich provides their children. Fundamentally, it means rethinking our still-persistent notion that educational problems should be solved by schools alone.

The more we do to ensure that all children have similar cognitively stimulating early childhood experiences, the less we will have to worry about failing schools. This in turn will enable us to let our schools focus on teaching the skills — how to solve complex problems, how to think critically and how to collaborate — essential to a growing economy and a lively democracy.

Ana has moved on from fractions into decimals.

Sat, 04 May 2013 15:04:11 GMT

It's hard going, but she's persevering. She had to do some work converting really easy fractions (1/4, 2/25, 1/20, that sort of thing) into decimals by converting to tenths or hundredths and then moving from there. She got through that, and when she was done I showed her the other way to convert into a decimal, by dividing. I said she didn't have to learn it now, as nobody teaches it until later, but it's pretty simple to do. And then, just for kicks, I showed her 1/3 as a decimal. After two iterations she was giggling uncontrollably, having seen the inevitable (lack of) end already. And here I was, calmly putting threes on the end of the equation and carrying down the zero, explaining that the reason they don't teach this until later has nothing to do with how hard or easy the work is, and everything to do with the fact that once you start converting fractions to decimals you sooner or later are bound to encounter 1/3. Or 1/7, or 5/12, or some other awful number.

She caught on fast, though, which really made us both happy.

Eva's teacher can't keep her in books, and she's now working her way through Harry Potter. She got tired of Ana's exclamations on the subject. Last book we read together was Cart and Cwidder, and the two of them have been discussing how to turn their wagon into a cart to travel around the world/city/block singing, or maybe not. It is both amazing and a little terrifying.

For sand tiger sharks, a deadly, cannibalistic battle inside the womb is part of evolution

Sat, 04 May 2013 11:50:53 GMT

http://wapo.st/12YTRG3

Something I must say is worse than what happens to baby hyenas.

20,000 people have already applied for the one-way mission to Mars

Sat, 04 May 2013 11:46:06 GMT

http://bit.ly/18eAk46

Well, going to Mars would be pretty great... but not if you have to be on TV, I think.

On the other hand, unlike the cast of Survivor et al., you'd be remembered for posterity, really remembered. Depending on your perspective that actually might be the same hand.

The Brazen Bibliophiles of Timbuktu

Sat, 04 May 2013 11:43:04 GMT

How a team of sneaky librarians duped Al Qaeda

http://www.newrepublic.com/article/112898