Here's something to stop and consider: You are mostly not you.

Ninety percent of the cells in your body don't have your DNA. They weren't in you when you were in the womb. Instead, they belong to trillions of tiny bacteria and other microbes that live in your stomach, your mouth and on your skin, among other places. Collectively, they make up between five and ten pounds of your body weight, a vast and teeming crew known as the microbiome.

Scientists have known about the microbiome for some time, but the advent of relatively inexpensive DNA sequencing has transformed the research, making it possible to sequence – and therefore identify – thousands of species of bacteria and other microbes at once.

The Human Microbiome: A Rogue's Gallery

What are these creatures living inside us? Find out here.

Among those doing the cataloging is Katie Pollard, a geneticist at the Gladstone Institutes in San Francisco.

Not long ago, Pollard was chatting with a few colleagues in a weekly meeting when one of them, a grad student named Chris Gignoux, mentioned some field work he'd been doing in a remote part of South Africa with an indigenous sheep and goat herding group called the Khoisan.

The Khiosan are thought to be the oldest genetic group on earth, ancestors of the rest of us. Even their language is unique, a “click” language with consonants found nowhere else in the world.

Gignoux is part of a team trying to piece together the Khoisan's evolutionary history by studying their DNA, which the team extracts from saliva samples collected during field research trips to South Africa.

But the scientists were running into a problem. The Khoisan samples were contaminated with non-human cells: bacteria and other microbes that live in the Khoisan's mouths.

“The exact DNA that they were viewing as contamination was very interesting to us,” says Pollard.

A garden in your gut

In recent years, scientists have come to see these bacteria and other microbes as a delicate ecosystem inside each of us. You can think of it as a garden in your guts, one you are constantly tending and adding to every time you eat a meal or are exposed to something in your environment.

And just like a garden, things can get out of whack. Invasive species take over; certain plants die off.

And when this happens, scientists believe, people can get sick.

Michael Fischbach is an assistant professor in the school of pharmacy at UCSF. He reels off a list of diseases that might – repeat, might — be connected to changes in our microbiome: “the inflammatory bowel diseases, including Crohn's disease. Possibly diabetes and obesity. Possibly even allergic diseases like asthma.”

This is new science. No one really knows. But Fischbach and others who study the microbiome are excited about the potential here, in part because of two recent discoveries.

Katie Pollard, a geneticist at the Gladstone Institutes in San Francisco, is working on cataloging the human microbiome. (Courtesy photo)

Fecal transplants and an unlikely connection

One was the announcement last year that people suffering from a stubborn bacterial infection called C.difficile were cured after receiving fecal transplants. They ingested fresh feces – collected from healthy donors and teeming with healthy bacteria – through a tube in their nose. It was a microbiome transplant, and it worked.

The second development came last month, when a researcher at the Cleveland Clinic published results connecting bacteria in people's guts to heart disease.

“Nobody would have put heart disease on that list,” says Fischbach.

He says the announcement sent ripples of optimism throughout the microbiome research community. “The notion that you could come up with something that is going to surprise even those who have been working on it for some time is very much in the air.”

Also fueling the excitement is the recent completion of the Human Microbiome Project, an effort, funded by the National Institutes of Health, to identify and catalogue the microbiota of 242 healthy American volunteers.

Now that scientists are starting to get a handle on what kinds of microbes live in the human body and, roughly, how those populations differ from one individual to another, a key question will be whether there is such a thing as an “ideal” microbiome.

In other words, if a bad, or imbalanced microbiome can make people sick, what does a good, balanced microbiome look like? What are the microbes that have evolved to keep us healthy, and how do they do it?

Was there a microbial Garden of Eden?

This is a hard question to answer because most of us have made huge, sweeping changes to our microbiomes at least several times in our lives by taking antibiotics.

David Relman, a professor of medicine at Stanford, was one of the first scientists to use DNA sequencing to study the makeup of the microbiome, using a swab from the inside of his own cheek.

Since then, his work has explored how antibiotics affect the microbiome, and how long those changes persist. He says while antibiotics have saved millions of lives, they’re a blunt instrument.

“In the past, we thought of antibiotics as magic bullets,” Relman says. “But – I hate using the military metaphor – they're more like a cluster bomb, or a neutron bomb. They're indiscriminate. And there's a lot of collateral damage.”

That collateral damage includes healthy bacteria, which may play important roles in digestion and other functions. Antibiotics can also create ideal environments for harmful bacteria to thrive.

Sometimes, the balance restores itself. Other times, the changes may be permanent. If a particular strain of bacteria is lost, it can't be passed on from one human generation to the next.

But this is hard to study. Because there’s almost no one out there who hasn't taken antibiotics. Which brings us back to the Khoisan.

Learning from the Khoisan

What occurred to Katie Pollard is that the Khoisan for the most part haven’t had that repeated antibiotic exposure. If researchers can find bacteria in the Khoisan that don’t show up in the saliva of industrialized groups, she says, “that would suggest that something in the modern lifestyle has potentially wiped out these bacteria.”

This work is just beginning. So far, Pollard's team has identified about 900 species of microbes in the Khoisan saliva. Next, they'll compare those species to samples from other populations to see whether there are any completely novel microbes in the Khoisan, microbes she and others haven't seen before.

Lest anyone start thinking that the Khoisan microbiome could be some sort of wholesale solution to modern ills (maybe imported through some kind of trans-Atlantic fecal transplant?) think again.

Among those 900 bacterial species identified, says Pollard, are several that you definitely wouldn't want, a fact that becomes clear when you look at photos of the Khoisan, many of whom are missing teeth.

“Many of the bacteria we've found are known pathogens,” says Pollard, “in terms of gum disease or enhancing plaque.”

Modern medicine has not been all bad for the microbiome.

Pollard and others who do DNA sequencing on gut microbes face a massive computational challenge, one that makes the human genome project look like a cakewalk.

But the end result, say Pollard and others, could be new insights into how we could tweak, even curate the bacteria in our bodies, to make ourselves healthier.

A small portion of Lake Berryessa, which would be part of a proposed National Conservation Area. (Photo: Craig Miller/KQED)

On one of those crystalline mornings so rare in California valleys, I joined a small group gathered in front of a coffee shop in the town of Winters, about 30 miles west of Sacramento. But we wouldn’t be lingering there over lattes.

"The plan for the day is to go up to Cold Canyon," announced Bob Schneider of the Woodland-based conservation group, Tuleyome. "We’re gonna hike up to the ridge for the views."

The views being sought were of what could become the nation’s newest National Conservation Area, tucked into the broad nether region between I-5 and Highway 101. Nearly 350,000 acres of federal land, the Berryessa Snow Mountain Conservation Area would get permanent protection from mining activity, sale to commercial developers and — it’s a bit unclear what else.

Tuleyome’s promotional handout calls the region a “largely undiscovered national treasure.” Michael Brune, the national head of the Sierra Club, agrees.

"It goes up about a hundred miles to the north to Snow Mountain and in between you’ve got got beautiful wintering habitat for bald eagles," Brune told me at a spot along Highway 128, overlooking Putah Creek.

Brune has thrown his weight behind the move to set aside this expanse. "Tule elk are here," he added, "You've got beautiful rolling hills on the western part of the valley."

Compared to the nation’s 16 existing National Conservation Areas, it would be among the biggest, a patchwork of lands variously managed by the Forest Service, Bureau of Land Management, and Bureau of Reclamation, pulling in three already-designated wilderness areas and a sizable chunk of the Mendocino National Forest.

"It’s a place that is close to Sacramento, close to the Bay Area, but very wild," says Brune.

Even if you make that hike up one of the ridges off the highway, east of Napa, the area stretches–literally–farther than the eye can see on most days. The Snow Mountain Wilderness Area is a hundred miles to the north. Down at the south end, the Conservation Area would encircle Lake Berryessa, a 16,000-acre reservoir and recreational magnet in this part of the state.

Talking with hikers and boaters around the lake, I found few who were even aware of the proposed NCA, let alone knew what it would mean. And that’s where it gets tricky. There seems to be no one set of rules for NCAs. Each one has its own "site-specific" set of protections and restrictions.

"I say this just doesn’t qualify," says Peter Kilkus, who publishes the Lake Berryessa News website from his 60-acre homestead overlooking the lake. He and some other landowners and business interests have opposed the NCA, saying it’s just not necessary. In February, the Woodland newspaper published an open letter to Yolo County supervisors from the head of the county's Farm Bureau, charging that an NCA designation "accomplishes little of merit, other than placing an additional layer of regulation over the affected area."

California’s first National Conservation Area was also the nation’s first — the King Range, along the stretch of northern California known as the “Lost Coast.” To qualify, lands are supposed to have “exceptional scientific, cultural, ecological, historical, and recreational values.”

"If you look at this proposed National Conservation Area — especially this south end at Lake Berryessa — this in no way falls under what would be suitable for an NCA in my opinion," Kilkus says. "It’s totally man-made, in the first place."

True, Berryessa’s not a natural lake. It was created in 1957 when the Bureau of Reclamation penned up Putah Creek with the 300-foot-high Monticello Dam.

Lake Berryessa was born in 1957, when the federal government built the 300-foot-tall Monticello Dam across Putah Creek. (Photo: Craig Miller/KQED)

"Before the lake was here, it was a huge farming community," Kilkus explains. "Then they built the dam, kicked all the people out. And they put in a lake. Even the fish are not indigenous." But down at the south end of Berryessa, the conflict doesn’t seem to be about fish.

To many, the thrum of jet skis and power boats is the pulse of the Lake Berryessa economy — an economy that has suffered in recent years, as an unfolding government snafu caused the shutdown of five of the lake's seven marinas. At first, the proposed NCA set off alarms that this kind of “motorized recreation” might be banned on the lake. Others worried that it might mean more restricted access to the lands themselves.

"It doesn’t affect anybody’s private property," Congressman Mike Thompson told me at a recent town hall meeting. "It’s federally owned property that will always be federally owned property."

This is the second time that Thompson, a Democrat, has put up a bill to designate this swath of land as an NCA. Barbara Boxer has a similar bill in the Senate.

"We’re providing this designation so all the federal agencies can better coordinate and better work together to get more bang for the taxpayer dollars," said Thompson. "Now how in the world anybody could be opposed to that is beyond me."

This time, lawmakers wrote in a promise not to mess with motorized recreation on the lake. That seemed to satisfy Marty Rodden, who runs the boat rentals at Markley Cove.

"I hope so," he told me, in between tinkering with outboard motors and casting off pontoon boats loaded with partiers. "Considering that this is how I make my living, and I’ll be out of business [if motors are banned]."

Rodden says he’s hopeful that once under a new multi-agency management plan, some of the abandoned resorts around the lake might come back.

"There’s a lot less going on up here," he reflected. "I believe there was about a million visitors a year, and we’re probably down to 250,000, so it’s taken a really hard hit on everybody."

Kilkus and others around Lake Berryessa are still skeptical. They’re concerned that once the land is redesignated, the government might yield to pressure from wilderness advocates and change the rules.

"If you read the guiding documents behind a NCA, it gives the government huge latitude to do almost anything they want," says Kilkus. "There’s still a lot of mistrust."

In Washington, the bill will confront another group of skeptics. It now runs the gantlet of congressional committees, including the House Natural Resources Committee, which has not been real receptive of late to designating new protected lands. A committee is expected to hear the Senate version sometime in May.

The proposed 100-mile-long National Conservation Area, from Lake Berryessa at the south end, to the Mendocino National Forest in the north. Green areas are managed by the US Forest Service, gold areas by the Bureau of Land Management. (Map: Tuleyome)

Tags: featured, lake berryessa
]]> http://science.kqed.org/quest/audio/another-try-for-californias-second-national-conservation-area/feed/ 2 38.6097407 -122.25404538.6097407-122.254045 A small portion of Lake Berryessa, which would be part of a proposed National Conservation Area. (Photo: Craig Miller/KQED) IMG_3019_crop A small portion of Lake Berryessa, which would be part of a proposed National Conservation Area. (Photo: Craig Miller/KQED) IMG_3402 Lake Berryessa was born in 1957, when the federal government built the 300-foot-tall Monticello Dam across Putah Creek. (Photo: Craig Miller/KQED) NCA_Map130305 A preliminary map shows the extent of the proposed 350,000-acre Berryessa-Snow http://science.kqed.org/quest/audio/brain-mapping-from-the-basics-to-science-fiction/ http://science.kqed.org/quest/audio/brain-mapping-from-the-basics-to-science-fiction/#comments Fri, 19 Apr 2013 21:50:49 +0000 Amy Standen http://science.kqed.org/quest/?post_type=audio_reports&p=52616

fMRI brain scans. (David Feinberg/UC Berkeley)

Get ready for the year – or the decade – of the brain.

President Obama recently announced what he called the next “Great American Project”: $100 million, plus private investment, to study what he called “that matter between our ears.”

Much of this work is already happening here in the Bay Area, where neuroscientists are starting small and dreaming big.

Cracking the Code

There's an idea about the brain that you hear a lot: That it’s akin to a language. If you could just figure out the meaning of every letter, you could read it and say – or do – anything.

“Think about what we could do once we do crack this code,” said President Obama in announcing his BRAIN initiative, which he’ll also have to sell to Congress.

“Imagine if no family had to feel helpless watching a loved one disappear behind the mask of Parkinson’s or struggle in the grip of epilepsy. Imagine if we could reverse traumatic brain injury or PTSD for our veterans who are coming home.”

But before any of that can be achieved – even if it can be achieved – we have to understand the brain first.

“The human brain is the most complicated known entity in the universe,” says William Newsome, a Stanford University professor of neurobiology and co-chair of the president’s BRAIN Initiative.

It's Newsome’s job to figure out what this mapping plan is all about.

"The most complex entity in the universe"

He says consider the numbers. There could be close to a hundred billion neurons, or nerve cells, in the human brain. And somewhere in the neighborhood of a thousand trillion connections, zapping little jolts of information back and forth from cell to cell.

Mapping at that level is not going to happen anytime soon, Newsome says.

“We are not going to solve and completely understand the human brain in ten years, or probably not even in 100 years," says Newsome. “It may take us a couple hundred years."

That’s a long time, which is one reason the project has been criticized as too vague.

If the goal of the BRAIN initiative isn't to fully map the brain or to cure a specific disease, what is it? And without a specific goal, how do you decide what kind of research to focus on?

It’s like trying to understand a beach. Do you count the grains of sand? Or study satellite photos of the entire coastline?

Somewhere near the satellite level is the work happening in UC Berkeley psychology professor Jack Gallant’s lab.

A graduate student named James is trying to stay as still as possible inside a functional MRI machine. When James squeezes a ball, the machine beeps steadily.

“It’s the sound of data,” Gallant says.

Mind Reading, Circa 2013

Gallant points to a computer monitor where, every two seconds, another crisp, black and white image of James’ brain refreshes itself.

“Here’s the cortex, the cerebellum back here. This is the brain stem, the thalamus,” Gallant says.

Using the fMRI, Gallant’s lab has been able to record what happens inside subjects’ brains while they watch movies, and then translate those responses into images.

These reconstructed videos are blurry but remarkable, about as close to mind-reading as we get in 2013. Gallant says in theory, this is just the beginning.

“In principle, it’s probably possible to reconstruct any activity in your brain that reflects ongoing conscious brain processes,” he said.

Any conscious thought could, one day, be visible to the outside world: a memory, a dream or your private, internal dialogues.

“We have this little person in our head that talks to us all the time,” says Gallant. “There’s no reason we shouldn’t be able to reconstruct that.”

As amazing – and scary – as this is, Gallant and others are quick to point out that the fMRI is full of limitations. For example, it doesn’t actually show neurons, let alone the connections between them. To be able to easily watch human neurons in action would take a machine that hasn’t been invented yet.

“If we knew what that technology will be, we would invent it today,” Gallant said.

So the BRAIN Initiative is almost certainly going to involve engineers building better machines.

It’ll also involve work that has seemingly very little to do with humans at all. This work is a lot closer to the grain of sand level.

Starting Small, Dreaming Big

John Ngai, director of UC Berkeley’s Helen Wills Neuroscience Institute, studies the olfactory system of – among other things – zebrafish.

Ngai wants to understand what happens in the brain of a zebrafish when it detects pheromones that signal danger. When the fish smell this pheromone, they dive to the bottom of the tank and hide.

Which of the zebra fish’s 100,000 or so neurons are driving this reaction and how?

If Ngai’s lab can figure this out, they’d have a working model for how information in a brain translates into behavior. And eventually not just for zebrafish.

Newsome, the head of the BRAIN Initiative, says fast-forward this line of work a generation or a few, and maybe you're closer to curing diseases like Alzheimer’s. Maybe you’ve even started to answer bigger questions.

Questions like, says Newsome, “why do I make so many mistakes that I know perfectly well are avoidable? Why do I hurt people that I love? Why do I turn left at some corner when I knew perfectly well that I should have turned right? What is it up there inside our head that produce emotions?”

Big questions that will have to start with very small answers.

A recent study estimates that close to half of human genes identified so far are already patented. The court’s ruling could put millions of dollars at stake for Bay Area universities and biotech companies.

At issue are two genes related to breast and ovarian cancer, BRCA 1 and BRCA 2. Women with mutations in these genes are five to eight times more likely to develop breast cancer. To gauge that risk, patients often get a genetic test. It’s one of the most common tests that genetic counselors handle, like Julie Mak at UCSF’s Cancer Centerin San Francisco.

Preparation for DNA sequencing (Maggie Bartlett, NHGRI)

“I do think it opens up a very loaded set of questions for people who are sometimes very young,” says Mak. “As you can imagine, the things we talk about with people are very serious and sometimes stressful and upsetting.”

A blood or saliva sample can tell a woman if she has those mutations, but that test isn’t run at UCSF. “For most BRCA 1 and 2 testing, the lab in Utah is the only one that does this testing,” Mak says, referring to Myriad Genetics.

Myriad Genetics holds patents on not only the test, but the actual genes themselves. That means one company has a monopoly on those genes and theoretically controls what can be done with them. That’s what’s being challenged by the American Civil Liberties Union.

Natural or Not?

“A lot of people wonder: how can you patent a gene?” says Mildred Cho, associate director of the Stanford Center for Biomedical Ethics.

In the case, the ACLU is arguing that genes aren’t patentable because they’re naturally occurring — they’re found inside our bodies. According to patent law, “products of nature are not patentable,” Cho says.

Myriad Genetics argues that by extracting a specific gene and isolating it, it turns into a man-made invention, which makes it patentable. “In order to analyze to DNA, you have to break open the cells and break the DNA up in to little pieces,” Cho explains.

Legal complexities aside, Cho says it has real effects on our healthcare decision, like getting a second opinion. “No laboratory has 100 percent accuracy and so you would ideally want to have a lab result that’s really important confirmed by another lab,” she says. “You can’t do that if there are patents on that lab test.”

Questions of Open Access

Patents can also affect genetic research, according to UCSF professor Dr. Robert Nusssbaum. When I meet him in his office, he’s wearing a button pinned to his shirt.

“So my button says ‘free the data,'” he points out.

Since DNA doesn’t come with an instruction manual that reveals if a genetic mutation is harmful or not, the only way to find out is to compare it to thousands of other genetic tests.

“The only way to make that happen faster is for all the laboratories to pool all their information in one place and all have access to it,” Nussbaum says.

But not everyone is sharing. “There are a couple of laboratories, and Myriad is one of them, that have decided that since they had the patent on testing, that they would keep their data locked up as intellectual property,” he says.

In response, Nussbaum has organized an open source database that holds genetic data about breast cancer mutations, free for researchers to use.

“In terms of gene testing, I think patents are of no value, period,” says Nussbaum.

Basis of Biotech

“Patents are a very important, fundamental part of the foundation on which the biotechnology, biopharmaceutical industry has been built,” says Sean Johnston, general counsel at Genentech in South San Francisco, one of the largest biotech companies in the world.

Companies like Genentech use genetic information to develop drugs and treatments, in addition to genetic diagnostic tests.

“Biotech and biopharmaceutical companies have relied upon patent protection to justify the significant investment, the risk-taking and the innovation that is necessary to develop new drugs,” Johnston says.

Johnston says it often takes a billion dollars to bring a drug to market, an investment that could be tougher to make without the protection of gene patents.

“It’s not a matter that if the court were to rule broadly our business would be destroyed,” Johnston says. “But in theory I think it has the potential to be very disruptive to the industry.”

Universities in the Middle

Biotech companies here aren’t the only ones watching this case. The University of California as a whole is one of the top ten gene patent holders in the country.

“Universities are often accused of patenting solely for the purpose of getting financial gain,” says Karin Immergluck of UCSF’s Office of Technology Management. The office handles several hundred gene patents.

“UCSF’s first goal is to translate our really exciting, cutting-edge technologies into products and services that will benefit the public,” she says.

The university walks a fine line. Companies pay millions of dollars a year to use its patents, like the one related to human growth hormone. But the court case brings up issue in licensing patents that universities already grappling with.

“For example, making sure the rights aren’t completely locked up in one company so that underinsured patients don’t have access,” says Immergluck.

Patient access, biotech industry profits and innovation could all be affected by the Supreme Court’s ruling. It’s expected in June.

Even when they're not receiving guests, curled wood shavings and girdled willow trees give the critters away. It started when a lone beaver was spotted in the Guadalupe River, just across the street from HP Pavilion in downtown San Jose.

Thrilled, the Guadalupe River Park Conservancy set up a trail camera to monitor its activity.

Then another beaver appeared.

“I jumped up out of my chair and high-fived my wife and hugged her when I saw the second beaver,” said Greg Kerekes of the conservancy, after going through the camera footage.

Soon, he discovered that three beavers, a pregnant mother and her two yearlings, were keeping house at the confluence of the Guadalupe River and Los Gatos Creek. A family indicates they will likely settle, said conservancy executive director Leslee Hamilton.

Environmental educators hope the beavers will stay because they benefit wildlife and can help teach children about watersheds.

“Eyes get really wide when children hear about salmon in the river,” Hamilton said. “The beavers will enrich our program and show kids what an ecosystem is.”

The Santa Clara Valley Water District has decided that the beavers do not pose a threat to flood protection efforts. Located near a water intake, Hamilton says the beavers could not have picked a better spot. If water rises to a certain point, it pours into an underground concrete channel bypass that leads to a flood control plain.

In 2007, a family of beavers also colonized Alhambra Creek in downtown Martinez.

“You could sit at Starbucks, drink your morning coffee and watch kits (young beavers) play,” said Heidi Perryman, president of Worth a Dam, a beaver advocacy organization.

Since the beavers have settled in Martinez, the ecosystem has flourished, seeing at least 13 new species.

“The next year, the river otter returned, no doubt to hunt the now plentiful fish in the beaver ponds. Then the year after, the mink returned,” said Rick Lanman of the Institute of Historical Ecology in Los Altos. “All manner of birds and fish have returned, and we don't even know how many species of dragonflies and damselflies.”

Beaver supporters praise the benefits that beavers bestow on the environment. The “ecosystem engineers” are a keystone species, and they raise water tables, create wetlands, clean water, slow water down and restore topsoil.

Lanman called beaver-created ponds “factories” for producing insects and fish, and “cafeterias” for birds and salmonids, such as trout and salmon.

Federally endangered species also benefit, such as the California red-legged frog and the southwest willow flycatcher. Beavers will cut down some trees and widen the amount of riverbank that gets watered, resulting in a net increase of trees, according to Lanman.

Armed with two industrial-grade incisors, beavers are often considered a nuisance. They cause problems with agriculture, damming irrigation canals and chewing trees. They also wreak havoc in urban areas, gnawing landscaping and flooding fields.

Beavers, North America’s largest rodents, are native to the Bay Area, but their numbers dwindled because of fur trading. In 1997, they were reintroduced to the Lexington Reservoir in Los Gatos, and the Guadalupe beavers arrived by swimming down Los Gatos Creek.

“A lost species has found its way back,” Kerekes said.

The beavers are starting to spread in the South Bay, a sign that the ecosystem may be able to support larger mammals again and that restoration efforts have been successful.

Norma Camacho, the water district’s chief operating officer for watersheds, said she is thrilled that efforts to improve the Guadalupe ecosystem are working.

Last year, a beaver was spotted in the Guadalupe River near Hedding Street in San Jose and another at the Sunnyvale Water Pollution Control Plant. In 2008, beaver tracks were also spotted in Charleston Slough near the Palo Alto-Mountain View border.

“They have been cruising the South Bay for awhile,” Lanman said. “The conversion of the South Bay salt ponds back to tidal marsh may be providing the beaver with a means to access the South Bay rivers. Beaver can cross salt water easily and even live in it if it's brackish.”

Perryman said people could see the beavers as a good sign for the river and its good fortune, adding that beavers revitalize ecosystems for free, unlike cities.

“A small investment in restoration continues to yield dividends,” Lanman said.

Sonar is known to disturb whales and can harm their hearing, a danger in an environment where sound is dominant. Sound travels four times faster underwater than it does in air, making it a powerful communication tool.

(Jason Isley/Scubazoo)

“The physical environment of the ocean really favors the use of sound and the animals have evolved accordingly,” said Brandon Southall, a marine scientist affiliated with the University of California-Santa Cruz. For the last few years, he’s been recording whales off California.

Blue whales use deep rumblings, almost too low for humans to hear. “Some of these low-frequency sounds can be picked up hundreds of miles away from where the animals are,” said Southall.

Other dolphins and whales use sound to locate objects in the water through echolocation. It’s a key tool for deep-diving beaked whales, a family of rarely seen and little-understood whales found off the coast.

“There’s a pattern of clicking that’s almost like a searchlight, where they’re flashing this strobe of sound,” Southall said.

Navy sonar technology is based on the same idea, but the sounds can be four times louder than a whale call, loud enough to actually harm whales and in rare cases, kill them. That happened with a group of beaked whales in the Bahamas in 2000.

“There were training exercises, military sonar training exercises, and shortly thereafter, an atypical number of animals washed up dead on the beach,” said Southall.

Southall studies the effects of sonar, work that’s funded in part by the US Navy. Most commonly, sonar disrupts marine mammal behavior – sometimes behavior that’s crucial to survival. Southall and his team have seen blue whales and beaked whales stop feeding because of sonar.

“We absolutely share the concern about protecting marine mammals,” said Alex Stone, an environmental program manager with the Navy’s Pacific Fleet. The fleet has done sonar training off Southern California and Hawaii for years. Beginning next year, commanders are looking to increase it.

“A training scenario may involve two or three Navy destroyers out looking for a submarine,” said Stone. The threat of submarine warfare decreased after the end of the Cold War, “but that trend has absolutely reversed and there’s been a proliferation of these very quiet, inexpensive diesel-electric submarines that a lot of countries have now,” including North Korea, explained Stone.

According to the Navy’s analysis, the sonar-training program could affect the behavior of whales, dolphins and marine mammals millions of times over five years. Stone says there are lookouts on board Navy ships that stop training runs if whales are spotted.

“We think that the mitigation measures are effective, but it’s true, you’re never going to see every marine mammal that’s there,” said Stone. “But in terms of impacts on species, we really haven’t seen any of those after years and years of doing these same types of training and testing activities in these same areas.”

“That’s always been a dubious argument but in light of new information it’s wearing especially thin,” said Michael Jasny of the Natural Resources Defense Council. “We now know that beaked whales off California are declining precipitously. We know that blue whales aren’t recovering.”

Jasny says the Navy should avoid key areas, like gray whale migration routes and the summer feeding grounds of endangered blue and fin whales.

“Southern California is a globally important feeding habitat for them,” said Jasny. “It should be elementary common sense to avoid the core feeding habitat of blue whales. “

The state of California came to the same conclusion in a review of the Navy’s plan. At a March meeting, the California Coastal Commission staff recommended the Navy stay out of sensitive areas.

“We rely on this large area and when you start to segment it in little areas where – you can go here, can’t go there – it really affects the training realism,” Stone responded.

Five years ago, California made the same request, but the Navy went ahead with the training anyway, citing national security concerns. The Coastal Commission sued and lost. This time, state officials didn’t mince words, like Commissioner Jana Zimmer.

“We’ve got this stumbling block of the Navy being completely unwilling – completely unwilling to accept any of the mitigations,” Zimmer said.

The Navy is also seeking approval from federal wildlife officials with the National Marine Fisheries Service. The agency is expected to make a decision later this year.

The Sinking Valley

Levee manager Reggie Hill calls this riverbed the Grand Canyon of Madera County. Its rapid erosion is caused by the land sinking downstream. (Sasha Khokha/KQED)

A meadowlark sings on a telephone pole, perched high above rows of gnarled grape vines in rural Madera County. But there’s another way to get a bird’s-eye view of these vineyards.

Reggie Hill unlocks a metal gate that opens onto the levees that rise more than twelve feet above the fields and orchards here. “Watch out for holes,” he warns. “There’s a lot of rodents out here.”

Hill is in charge of 191 miles of levees along the lower San Joaquin River, which can flood in big snowmelt years. Federal and state officials check to make sure these berms are high enough to protect crops, farmhouses and schools. But over the last few years, Hill says, something strange has started to happen.

Subsidence in the Central Valley. Click to see a larger version of the map. (USGS)

“They came out here, did a survey,” he explains, “and then the next time, came out to finish up their survey, none of their elevations matched. Took them a while to figure out it isn’t that we made a mistake, the land is changing.”

Measurements show the land here is sinking about a foot a year, as thirsty cities and farms pump water from aquifers that lie deep underground, below a thick layer of clay.

Chasing Water

“The more demand for water, the deeper they’re starting to chase the water,” says Hill. Wells in this part of the Valley that used to find water 300 feet below ground level, now reach down nearly 900. "They’re chasing water," he tells me, "and what happens is they start pulling water out from under these clay layers, and these clay layers collapse. And it can’t come back.”

That rapid sinking, called subsidence, is some of the fastest ever measured in the Central Valley, says Michelle Sneed, a hydrologist with the U.S. Geological Survey. “A foot a year is quite fast, and hard to engineer against for things like bridges and dams and roadways,” says Sneed.

But what if there were a way to both keep the Central Valley’s taxed underground aquifers from drying up, and the land from sinking?

The Flooding Fields

About an hour’s drive south of our levee, on the huge farm known as Terranova Ranch, powerful electric pumps draw well water for about seven thousand acres of crops like tomatoes, grapes, almonds and pistachios. Manager Don Cameron says his electric bill tops a million dollars a year, in large part because those pumps have to work so hard to pull groundwater from wells hundreds of feet deep.

"We’ve seen declining water tables over the last 30 years that I’ve been here,” says Cameron. “And we want to do something to change that.”

Terranova Ranch sits southeast of Fresno in the King’s River basin, an area where farmers are pumping unsustainable volumes of water in dry years. At the other extreme, farms and communities here risk floods when rivers are pulsing with too much water.

A flooded field at Terranova Ranch. (Phil Bachand and Don Cameron, Terranova Ranch)

Terranova is experimenting with a way to address both problems. The idea is to capture excess river water in the occasional big water years, diverting it directly into crop fields, where the water will sink into the ground, and recharge the aquifer.

“We’re putting it away when there is flood water available, and essentially storing it underground, rather than building a new dam somewhere, which is pretty unlikely in this day and age,” says Cameron.

This is a little different from conventional groundwater “banks,” where farmers share water from an underground aquifer, or buy it from each other. This is an experiment in “banking” water right on the farm where it’ll be used.

Two years ago, Cameron worked with environmental engineers and state regulators to flood about a thousand acres of farmland with a foot of water from the Kings River. The water pooled up in the fields, making vineyards look like rice paddies. And that raised a few eyebrows around here.

“There have been a lot of growers that have looked at our operation with skepticism,” says Cameron, recalling one test that left his grape vines under about a foot of water for three months. "The vines eventually turned a yellow color and we turned the water off, and about a week later, they were back to normal.”

And they still produced grapes — with excess river water that otherwise would have flowed out to San Francisco Bay.

The Catch

The state Department of Water Resources has awarded a grant to Kings River water managers to try and replicate this project more widely starting this year. Meaningful recharge of the aquifers would require a large-scale, coordinated effort. But there’s a catch: it might not work everywhere.

Sneed, the USGS hydrologist, says deep under some farms in the San Joaquin Valley are continuous swaths of what’s called “Corcoran clay.” And if you put water on top of that, it could make things worse.

“It could backfire,” says Sneed. “It really depends on the geology of the area whether that is a good solution or not.

Because if water flooding into the fields can’t penetrate through the dense Corcoran clay, it can’t recharge the deepest aquifers where farmers are pumping the most. And the weight of the water pushing down on that clay layer could make the land sink even faster.

Aerial view of Devil's Slide tunnel project. Credit: Carwil / Wikimedia Commons

It's been a long time coming. The first highway tunnels to open in California in nearly fifty years are about ready for motorists.

Two mile-long, state-of-the-art tunnels will offer a new route to what has been a stunning, cliffhanger of a drive along Highway 1 above Northern California's coast. The passage, between Pacifica and Half Moon Bay, has been the site of so many landslides, prolonged closures and deadly car accidents that it earned the name, "Devil's Slide."

Photo: Jenny Oh

The new tunnel consists of two bores each about 4,200 feet long with one lane and wide shoulder. The cutting edge tunnels have been a major engineering project and will feature jet-powered exhaust fans and carbon monoxide sensors. That's much more high-tech than Cal Trans' last tunnel, the third bore of the Caldecott Tunnel, which opened in 1964.

Photo: Jenny Oh

After five decades of political and environmental roadblocks, the 439-million dollar federally funded project is finished. Its opening will roll out over two days. Opening ceremonies for the twin tunnels and accompanying bridges is Monday, March 25th. The tunnels will be ready for commuters the following morning. The old Devil's Slide stretch of California coastline will soon open up to hikers and bike riders.

Photo: www.dot.ca.gov

The Bay Observatory is in a newly-constructed part of the building. There are views of San Francisco Bay on one side, and the Transamerica Pyramid on the other. (David Livingston/EHDD)

Packing up exhibits at the Palace of Fine Arts, the Exploratorium's former home. (Joshua Cassidy/KQED)

There will be outdoor exhibits on the pier, portions of which will be open to anyone — you won't need tickets to the museum to see them. (Courtesy Zum)

Pier 15 used to be a commercial pier, and it holds onto that character, including signs painted on the wall by previous tenants. Below is the mostly-glass Bay Observatory. (Courtesy Exploratorium)

Exhibits in the Bay Observatory emphasize the world around the museum, like this "landscape scope," an iPhone mounted on a spotting scope typically used by birders, that brings the Bay Bridge up close. (Jenny Oh/KQED)

Read and hear more about the move and the Exploratorium's new building.

A drawing of the Exploratorium at Pier 15 by lead designer Marc L'Italien of the firm EHDD.

After forty-three years in the Palace of Fine Arts near the Golden Gate Bridge, the Exploratorium is moving to a restored pier on the Embarcadero. The move is a big experiment for the museum: how to grow into its new location, without losing the feel of its old self.

Leaving the Roman Ruin

The Palace of Fine Arts is a rosy-colored faux-Roman ruin, sitting next to a pond popular with swans and brides. Stepping inside was always a funny juxtaposition: going from the Fantasia on the outside, in, to the din of the Exploratorium. In its old space, the museum was a buzzing, windowless warehouse, centered around a shop where museum staff figured out how to hack together its hundreds of quirky contraptions that help teach kids scientific concepts and where everything had a familiar, “do it yourself” feel.

"When I first took this job, a designer friend of mine said, 'So you gonna clean this place up?' And I said, 'No, please.'" laughs Tom Rockwell, the director of exhibits at the Exploratorium. He took the job knowing it would eventually involve a move. But he says, it’s not about “cleaning the place up.”

"To me, one of the key jobs has been not to lose the funkiness," he says. "Not to lose the sense of it being like an inventor’s garage, where people are constantly making things and discovering things. And you know, inventors don’t worry so much about whether the cabinetry all looks perfect."

One day a few weeks before the facility closed in January for the big move, project manager Owen Lawrence was dressed in white coveralls, vacuuming a piece of the listening cloud exhibit before it got packed up.

"I don’t think anybody realized how much dirt was here," he says. "Normally I’m doing budgets and timelines. So it’s kind of an all-hands on deck thing right now. So I've got my Tyvek suit on. I've got my gas mask."

The Upgrade on the Embarcadero

The new Exploratorium is a stunning, $300 million facility on the San Francisco waterfront at Pier 15, triple the size of the old museum.

The new site includes a restored pier and new construction (Courtesy of Zum)

One reason for the move was to be more accessible: the new location is easier to get to on public transportation, and close to downtown. Planners are hoping that will improve attendance. The Exploratorium has about 600,000 visitors a year now, half the annual total of the Ontario Science Centre in Canada, which is a similar museum. And there’s the California Academy of Sciences' new building in Golden Gate Park, which has overshadowed just about everything else in San Francisco.

Then, there are other things that could just work better.

"When you needed air conditioning in the old building, we would buy an air conditioning unit for, like a house, and bolt it to the wall with plywood," says Chuck Mignacco, building operations manager. We're standing in front of the new building. There are still active piers nearby, but this one is now a state-of-the-art green building. And he is excited about it.

"Think of the building like a living thing," Mignacco explains. "This one, unlike the old one, has a brain and a computer in it."

The goal is for this new building, which will have 600 exhibits, to be net-zero energy — to produce as much electricity as it consumes. There are 85,000 square feet of solar panels on the roof, and on the inside there's the Bay Water Room, part of the mechanical system for the building. The colorful pipes in the room suck water in from San Francisco Bay, which — since we’re out on a pier — is directly below our feet. The cold water helps regulate the temperature of the building – it cools off the warm spots and then distributes the heat to cooler places.

So the building is kind of a science experiment in itself. Marc L’Italien, from the San Francisco-based architecture firm EHDD is the lead designer on the Exploratorium, and he says, that's part of how net-zero energy buildings work.

An artist's rendering of the Central Gallery in the new building, where exhibits will focus on sight and sound. (Mark Pechenick/Exploratorium)

"You have to tinker with them and Exploratorium staff are born tinkerers," he says.

The museum in this new building still has a warehouse-y feel: concrete floors, big open spaces.

"We see the architecture as the straight man," says L'Italien. "They steal the show with the punchline, with the exhibits."

L’Italien and his team spruced up the exterior and restored signs from previous businesses on the old pier.

"I think Pier 15 in its day wouldn’t have been a building that people would have taken much notice of," he says. "And now the fact that you have a world-renowned institution like the Exploratorium here, it’s going to get a lot of people visiting, and we’re celebrating the history of this site, of San Francisco with this building."

New Site, New Science

New exhibits take advantage of the site, too. The Bay Observatory is part of a newly-constructed wing of the museum, a transparent-feeling room with floor-to-ceiling windows giving big views of the Bay on one side, and downtown San Francisco on the other. Sebastian Martin, an exhibit developer working on the Bay Observatory, fiddles with an iPhone mounted on a spotting scope.

"We call this the landscape scope," he says. "Right now I’m looking at a spot over at Treasure Island. I’m actually looking at the water."

He's been using the scope to watch water currents change. Other exhibits here examine the sun, weather, wind direction and tides, and there's a computer that identifies ships as they go by.

"I think when we first visited the piers we all realized what an opportunity this was for us to explore the world around us, rather than the kind of world in a kind of test tube," says Susan Schwartzenberg, who works with Martin on the Bay Observatory.

Physicist and teacher Frank Oppenheimer founded the Exploratorium in 1969. (Courtesy of the Exploratorium)

Sticking With a Tradition of Staying in Flux

Some things won’t change. The shop is still in the middle, and familiar exhibits like the tornado are here, too. The old tactile dome didn’t make the move, but they're building a new one.

The Exploratorium has been a pioneer in the world of interactive, hands-on science education for over four decades. And when it's ready to unveil its new home, Rockwell says, it will still be a work in progress.

"We keep on reminding ourselves we don’t want to open too finished," he says. "We have a lot of projects that we will open with prototypes, with things that we’re going to start learning from and then keep on changing and evolving as we go."

The Exploratorium is scheduled to reopen to the public — prototypes and all — on April 17.

See More photos and images of the new building.

Chuck Reed, named ‘Green Mayor” by former California Governor Arnold Schwarzenegger, shows off solar cells designed by local companies. (Photo: Alison van Diggelen/Fresh Dialogues)

Silicon Valley is well known for being the cradle of tech innovation, but its largest city, San Jose, wants to claim the title as the world center of cleantech innovation too.  In 2007, the city launched its green vision, a 15 year road map to make San Jose one of the nation’s greenest. City leaders have just released a report card on their ten ambitious goals at the one third marker. Let’s take a look at their green progress; and its impact on the local economy and the environment.

Green mayor, green building

Mayor Chuck Reed sits in a sunny corner office on the 18^th floor of San Jose’s City Hall, the first city hall in the nation to achieve a platinum certification, the highest green building award. He’s looking through a new report on how the city is doing. Five years after announcing his ambitious green vision plan, the city is on track to reach its goal of creating 25,000 new cleantech jobs by 2022.

San Jose's City Hall received its LEED Platinum Certification from the US Green Building Council in 2009. It incorporates abundant natural light to reduce the need for electric lights. (Photo credit: City of San Jose)

“We started down this road trying to tie the environment and the economy together. So having 10,000 cleantech jobs is a big plus,” Reed says.

The nation’s 10^th largest city has nine other goals, including one to divert 100% of its trash from landfills. San Jose is currently diverting 73% of its trash. This compares to San Francisco’s reported figure of 80%.

Already a plastic bag ban in San Jose has reduced bag litter by 89% in the storm drain system and the city council is moving toward banning Styrofoam containers.

Ambitious Goals

One of San Jose’s most ambitious goals is to get all of its electricity from renewable energy. With 10 years to go before the deadline, it’s reached just over 20% and needs to accelerate progress.

“That’s going to mean radical changes, but this is a valley that does things in radical ways,” says Carl Guardino, president of the Silicon Valley Leadership Group (SVLG), which represents hundreds of local businesses.

“Silicon Valley and San Jose Mayor Reed sets audacious goals,” adds Guardino. “If we fall a little short, just think of how far we would have come.”

San Jose has helped change national standards for LED street lights and is now saving thousands of dollars using efficient, dimmable street lights.  Yet it’s only replaced 4% of its 62,000 lights.

Using other people’s money

Despite making progress, it’s been a tough road through the recession. Like most U.S. cities, San Jose has faced severe budget constraints and was forced to be innovative in funding its green vision.

The city has managed to leverage more than $100 Million in federal tax credits and private and public funds to move forward.

“I said from the beginning that the key to being able to succeed with our green vision was to work with other people’s money,” says Mayor Reed, who is known for his pragmatism.

Of course, it helps to be located in the center of one of the country’s most innovative regions, according to Kim Walesh, director of economic development for the city.

Kim Walesh, Director of economic development at the City of San Jose explains how the city's location within the Silicon Valley ecosystem offers strategic advantages for economic growth and innovation. (Photo: Alison van Diggelen/Fresh Dialogues)

“Being the large anchor city in Silicon Valley, we are remarkably open to new ideas, to thinking differently and we’re scrappy, so we know how to pull resources together toward a common goal and leverage, leverage, leverage,” says Walesh.

The city has certainly leveraged its sunny climate. According to state regulators, San Jose has installed more solar panels on its private and public buildings than any other California city.

“Southern California sun doesn’t hold a candle to our aggressive goals for solar installations in sunny San Jose,” says a jubilant Walesh.

The challenge of higher hanging fruit

But others, like Megan Medeiros with the Loma Prieta Chapter of the Sierra Club, paint a less rosy picture.

“San Jose has already picked off the low hanging fruit of their green vision,” says Medeiros, who feels the city has prioritized productivity before efficiency.

She’d like to see a lot more energy efficiency measures like green building taking place. So far, the city has only built, or retrofitted, 13% of its goal of 50 Million square feet of green (private and public) buildings.

San Jose is doing better with its efforts to cut per capita energy use in half; it’s 25% of the way to its goal.

Medeiros suggests San Jose adopt Palo Alto’s carbon neutral goal or try to take the lead in alternative transportation like San Francisco has with its popular car share communities and mass transit system.  But San Jose has had some success with its own public fleet of vehicles: 40% now run on alternative fuels.

Medeiros would like to see San Jose building more pedestrian and bicycle paths and planting more trees.

Megan Medeiros, Development Manager at the Loma Prieta Chapter of the Sierra Club says San Jose needs to make it easy for people to get around on foot, bicycle and by public transportation. (Photo: Alison van Diggelen/Fresh Dialogues)

If it did that, it could be attracting a lot of younger people who, Medeiros says, are “flocking to San Francisco” because it provides them with a better quality of life.

The economic impact of green

But SVLG’s Carl Guardino praises cities such as San Jose that have taken big steps toward more sustainable economic growth.

“Both San Jose and San Francisco, they have taken tremendous strides, along with Mayor Bloomberg in New York, in being on the cutting edge of innovation, of the green economy, working as a public sector to bolster private sector success,” he says.

San Jose’s Kim Walesh points out that cleantech jobs are an important new driver of the local economy. She cites last year’s Milken Institute report, which described the San Jose metro area as the nation’s number one performing city in terms of jobs and wage growth – thanks to its innovative tech culture. The San Francisco metro region ranked 36.

“We’re not a splashy city that makes a lot of announcements,” says Walesh. “We’re a city of idea generators who also implement. We can talk about the green vision, but we’re really walking the green vision and we’re making some progress.”

Looking to the future, San Jose city officials are abuzz about this summer’s opening of its Cleantech Innovation Center. It’s a partnership with Lawrence Berkeley National Lab and will offer a demonstration center for cleantech startups to test, showcase and speed commercialization of their green products.

To see all of San Jose’s green goals and how it’s measuring up, check out San Jose’s Green Vision Progress Report for 2012.

Path of two 35-mile tunnels through the Sacramento-San Joaquin Delta. (Graphic: Bay Delta Conservation Plan)

More details have emerged on a $23 billion plan for California’s trickiest water problem: the Sacramento-San Joaquin Delta.

State water officials are proposing a pair of tunnels through the Delta, which supplies water to two-thirds of the state’s residents. That water supply will depend on thousands of acres of habitat restoration to bring back endangered fish.

Thursday’s release was more a trickle than a flood, with just a third of the several thousand-page plan unveiled. But to Chuck Bonham of the state’s Department of Fish and Wildlife, it was a victory.

“Many have said it would never come out,” he said. “Some have said it couldn’t come out. It’s out.”

The Bay Delta Conservation Plan is designed to meet two “co-equal” goals, as they’re known. First, to reverse the decline of the Delta’s endangered fish, some of which have suffered steep declines in recent years. Second, to supply cities and farms across the state with water, something that’s been a sore spot recently.

“Because of the presence of Delta smelt this year and also of migrating salmon, we had to reduce deliveries, or exports, from the Delta on the order of 700,000 acre-feet of water,” said Mark Cowin of the Department of Water Resources. Water managers reckon an acre-foot to be about what a typical suburban household uses in a year, though many western households use less.

Cowin says similar cutbacks could be prevented in the future with two, 35-mile water tunnels that would run under the Delta. The tunnels would withdraw water farther away from sensitive fish.

That doesn’t mean the state gets all the water it wants. “This plan does not include any guarantees for water supply deliveries,” Cowin said. According to modeling, the project would export 4.8 to 5.6 million acre feet of water a year, close to the historical average but not as high as several recent years.

The supply also depends on more than 100,000 acres of habitat restoration, including tidal marshes that could help endangered fish recover. The restoration work would be unprecedented for the region. “We’re talking about restoration potentially observable from space,” said Bonham.

This draft follows a previous version released in 2012 that was criticized by state and federal wildlife officials, who said it didn’t do enough to protect endangered fish.

Bonham says the new plan reflects that feedback. “These goals and objectives are specific at a level that I don’t think we’ve been talking about in the Delta before,” he said. Changes notwithstanding, many residents and lawmakers from the Delta continue to oppose plan. “This draft Bay Delta Conservation Plan (BDCP) continues to ignore the very real concerns expressed by northern California stakeholders," wrote Congresswoman Doris Matsui (D-Sacramento) in a joint statement with several other legislators opposing the tunnels.

The $14 billion dollar tunnels would be paid for by water agencies, while the public would be on the hook for habitat restoration. More details on the costs are expected next month.

Killer electrons aren’t a threat to life on the ground, but they are a concern for the more than 1,000 satellites orbiting the planet. Satellites we depend on for everything from storm warnings to GPS navigation to TV programming.

A diagram of the Earth's radiation belts, where killer electrons are found. (Image: NASA/Van Allen Probes/Goddard Space Flight Center)

“Every major sports event — certainly every Olympic Games, the Super Bowl as well as the Academy Awards,” says Jean-Luc Froeliger, describing events carried by his company, Intelsat, a global satellite operator.

Scrambling Satellite Data

One thing Froeliger knows: space is not a dull place.

“In April of 2010, we had an event on our Galaxy 15 satellite,” says Froeliger. “We were sending commands to the satellite but the satellite was not accepting any command.”

Galaxy 15 had become a $100 million zombie.

“The satellite started to slowly drift,” says Froeliger, potentially interfering with satellites around it. Intelsat worked for months to reboot Galaxy 15, just about all that can be done with a satellite 22,000 miles away. Eventually, it came back online.

Froeliger says it’s all part of operating in the harsh environment outside our planet. “Satellites are constantly bombarded by high energy particles that flow from the sun,” he says.

Our sun sends out a stream of charged particles called the solar wind. This year marks a solar maximum, the peak of the sun’s activity, which can have big effects on our planet. “When those particles come close to the Earth, they get trapped by the Earth’s magnetic field,” Froeliger says.

Picture the Earth as a donut hole, and the magnetic field as a giant, invisible donut around it. The charged particles trapped inside the field create radiation belts. Galaxy 15, like other geosynchronous satellites, flew right through the belt and was bombard with charged particles, which created a short circuit.

The BARREL team launches one of 20 research balloons over Antarctica. (Photo: NASA/S. Spain)

But even just one particle – a single electron – can cause problems. “Some of them can penetrate metal and they can damage the electronics inside the satellite,” Froeliger says.

At least once a month, a killer electron goes through a satellite’s exterior and hits a computer chip inside. “The data that is stored in the computer gets corrupted,” says Froeliger, causing temporary or permanent damage.

Studying Electrons in New Detail

“Why they call them killer electrons is because they can penetrate several millimeters of aluminum or steel and get to you,” says David Smith, a physicist at the University of California, Santa Cruz.

Smith is standing on the roof of a four-story building on campus, where a small shed is used as their mission operations center.

“What we’re studying is electrons that come slamming down onto the atmosphere from Earth’s radiation belts,” he says. The electrons are stopped there, but Smith says you can still see their fingerprints.

Smith and his colleagues with the BARREL project have launched large research balloons to look for electrons falling out of the magnetic field. The balloons are released from Antarctica and travel 20 miles up, sending data back to UCSC.

Smith says understanding the risk from killer electrons is tricky because their numbers are constantly in flux. “On a given day, you may have a thousand times more of these very high-energy electrons in the belt than you did a few days previously.”

They’re also mysterious because killer electrons don’t start out as killers. Electrons arriving from the sun are low-energy for the most part. “It’s after the Earth captures them that something ramps them up to these really high energies,” Smith says.

To find out what that something is, Smith and his team are collaborating with a new NASA mission. In August, NASA launched the Van Allen Probes, two satellites designed to take detailed measurements inside the radiation belts.

In December, the probes made a recording of a mysterious phenomenon in the radiation belts: electromagnetic waves. “We’ve known about these waves for quite a long time but we’ve never had the kind of measurements that we needed to really understand them,” says Craig Kletzing of the Van Allen Probes mission.

Scientists theorize that the waves could be responsible for accelerating killer electrons. “The waves give energy to particles much like a surfer,” Kletzing says. Think of the waves as the ocean and the electrons as little surfers.

These results and others from the mission are expected to give scientists a better understanding of the Earth’s radiation belts. That could lead to better forecasts about when they’re particularly dangerous – something that’s key for NASA and for the satellites we depend on.

Planners have spent decades searching for a fix. But they'll have to finish the job without the advice of a man who’s played a central role in Delta science.

Jeffrey Mount, a retired UC Davis scientist, was dubbed “Doctor Doom” for his dire pronouncements about the Sacramento-San Joaquin River Delta. (Photo: Craig Miller/KQED)

Jeffrey Mount, the scientist dubbed “Dr. Doom” for his dire pronouncements about the Delta, has retired from his post at University California, Davis. Science editor Craig Miller caught up with him – where else – on the river, aboard his 27-foot cruiser, “Tugnacious.”

This is an edited version of their conversation.

The question of what to do about deteriorating conditions in the Sacramento-San Joaquin Delta has dogged Mount throughout his 33 years as a professor of geology, as co-founder of the Center for Watershed Studies at UC Davis and going back to Governor Brown’s first administration. I asked Mount – one of the Delta’s most plainspoken explainers, why it matters so much.

Craig Miller: Eight in 10 Californians can’t even tell you where or what the Delta is. Why do they need to know?

JM: Very few Californians get the notion that this is an interconnected system now, with water that comes all the way out of the Trinity River, piped over and into the Sacramento River and down through the Delta, run into canals and ends up in San Diego. I mean really, that’s extraordinary, all the way from the Klamath Basin to San Diego. This is an interconnected network, so 25 million people get some of their water out of the Delta.

An aerial view of the Sacramento-San Joaquin River Delta.

CM: You said in an interview that you thought we were down to our last shot with the Delta. What did you mean by that? And what do you think the real chance is that we'll have a long-term solution in hand by, say 2020?

JM: Let me explain why I think we’re down to our last shot. We have deeply entrenched interests, and regrettably it’s not simple. You’ve got farmers fighting against farmers. You have urban interests fighting against urban interests. You have environmental groups fighting against environmental groups, and then they’re all fighting each other, and that makes it wickedly complicated. And instead of coming out of their foxholes, they seem to be digging deeper and deeper foxholes.

The Sacramento-San Joaquin River Delta network.

Events will eventually dictate how we manage the Delta and I have said many times, and nothing in the last seven or eight years has changed in this, that we’re dealing with a system that is unstable, and it will rearrange itself, whether from floods or earthquakes or rising sea level or changing human demands on the system or invasive species, it is unstable and it is changing and if we don’t get our hands around it now, it’s going to be doubly hard to get our hands around it in the future.

Some believe one way to “get our hands around it” is to move southbound water around this fragile ecosystem – or in the case of the latest proposal, under it, with twin tunnels that would shuttle water from upstream on the Sacramento, more than 30 miles south to serve needs in the Central Valley and Southern California. Mount agrees, saying it’s the only way to comply with current laws that put water needs and the environment on equal footing.

JM: To meet the co-equal goals of the 2009 legislation, I think you’re going to have to have a tunnel or two. Don’t like it, go back and change the policy. You could say, "We’re going to manage this ecosystem. We’re going to go for ecosystem health as the primary objective within it." If that’s the case, at best you want a tiny little pipe – a peripheral garden hose would be the best description of it. You want to dramatically reduce your withdrawals from the Delta, both in-Delta exports and then all those people upstream; all those people like San Francisco, let’s take them for example, they’re taking water from the Delta, they’re just taking it out upstream.

CM: By upstream, you mean up in the Sierra.

JM: Yeah, they’re just taking it out before it gets to Delta, that’s all.

A canal in the south Delta, sending water to the Central Valley Project.

CM: Give me your pithiest version of why a tunnel beats a canal.

JM: Actually I don’t think there’s any difference between the two in terms of system performance, but there are major differences politically. Good luck building a peripheral canal across the Delta given the level of local resistance and changes in our practices of eminent domain. I can completely understand why they want to spend more money and go under the problem rather than over the problem.

CM: We talked a little about this déjà vu aspect of it, this goes further back than Jerry Brown’s first term, this goes back to Pat Brown, doesn’t it?

JM: That’s correct. When the state water project was developed, they knew all along that they had left a hole in it, and that is the Delta. They knew there was a problem even back in the 1950s that the Delta was going to be a major issue. From that point on, this intractable, difficult wicked problem has bedeviled governors, heads of the Department of Water Resources and water managers in California nonstop.

CM: If they were so aware that this was a problem looming, why didn’t they address the problem head on the first time around?

JM: There’s a tendency in water supply to leave the most complicated and difficult problems to later. We are a society – and there’s no difference in the water supply community – that likes to pluck the low hanging fruit and put off the hard work until later. The Delta fix, if there is one, is not simple, it’s not cheap, it involves burning massive amounts of political capital to get it done, and it involves lots of angry people no matter what you do. I can easily understand why people kept putting that one off.

And yet, with all of the rancor that remains in the Delta water wars, Mount sees a light at end of this tunnel.

JM: I can actually say that I think the state government and federal government are starting to paddle together, which has not been the case – it’s actually been one of the principal problems. They are actually starting to look like they’re much more in sync with each other, and that’s a glimmer of hope.

CM: Does that mean you think we have a decent shot at a long-term solution?

JM: I think it’s a 50-50 chance that we’ll get a long-term solution out of this. This is all of California’s problem. I mean this is 25 million people, also two-thirds of the population of California. It’s our problem.

Mount still has some skin in the game. In his new career is as a consultant, he says he wants to help restore rivers, not just talk about restoring them. As for his nickname, “Dr. Doom,” Mount says it was coined a decade ago by then-KQED reporter Tamara Keith, now Capitol correspondent for NPR. It stuck – and Mount still embraces it, though no doubt he’d love to be proven wrong.

Sean Greene contributed to this article.

Brianne Brawley, a scientific aide with the Department of Fish and Wildlife, holds herring samples. (Photo: Shannon Service)

If you are a seafood lover, you are no doubt aware when the salmon or crab season begins. But late February marks the end of herring season. Herring are one of those small silver fish unceremoniously referred to as “bait fish.” Small fish like herring are the critical base of the marine food chain and, without them, there would be no bigger fish.

Not that long ago California’s herring population came perilously close to collapse. While their numbers are increasing, herring in the Bay are still struggling to return to their once prolific numbers.

The Fleet

San Francisco’s herring fleet is the last commercial fishery that chases its fish almost exclusively in San Francisco Bay. Captain Ernie Koepf has plied the Bay in his boat, The Ursula B, for 35 years. He offloads six tons of herring on a cool Monday morning behind Pier 45. Little shimmery scales line his wool cap.

The herring is sucked out the boat’s hold by a giant orange vacuum that then spews it onto a conveyor belt while dozens of screeching gulls hover overhead. From there, the fish is dumped into boxes full of ice, shipped off — often overseas — then ripped open to get at the golden eggs, called roe, that are a delicacy in Japan.

Near Collapse

Four years ago, there almost was no roe to enjoy. California nearly lost its herring population. Scientists believe a lack of food sources in the ocean and warming water caused the numbers to shrink by ninety percent. Government decisions to close the herring season and impose strict catch limits helped to bring back some of the herring, but now there is a new problem: The little silver fish are getting inexplicably tinier. It’s getting tougher to find older, more valuable herring.

“In fact, there’s been a very, very dramatic decrease in the age distribution of the population,” says Audubon biologist Anna Weinstein.

“So what that means really is that the herring that are spawning now in San Francisco, and other parts of California, are almost all two and three year-old fish. Well, what’s wrong with that? This is a fish that lives to be 10 to 13 years old and is a multiple year spawner and the eggs of older fish tend to be better quality eggs. A whole population made up of younger fish is a classic sign of stress in fisheries.”

Gulls swarm as the Ursula B offloads six tons of herring near Fisherman's Wharf. (Photo: Shannon Service)

Signs of stress in herring have conservationists like Weinstein worried. Herring is a critical food source for the ocean’s bigger fish. These little fish, also known as forage fish, are in decline globally. In fact, some conservation groups are so concerned about the state of West Coast anchovy and sardines, that they took the National Marine Fisheries Service to court this month in San Francisco. The suit is asking for stronger fishing regulations on forage fish.

While herring aren't included in the current lawsuit, Audubon and Earthjustice have expressed concern about how California’s Department of Fish and Wildlife are managing the state's herring stock.

“It’s definitely something the department is concerned with,” says Fish and Wildlife's Tom Greiner. He and his team fish for herring samples on the Bay to take back to the lab. But Greiner says the mystery of the missing older generations isn’t unique to San Francisco — which makes solving the problem tricky.

“It’s actually a coast-wide concern,” he says. “Including areas that aren’t even fished. So if we only had it in fished populations, then we’d assume it was overfishing. But the fact we’re seeing it in populations with no fishery makes us think there’s a different cause. We’re not sure”

To make matters worse for San Francisco’s herring fisherman, prices for roe in Japan are sliding. It’s partly competition from herring fishermen in Canada and Alaska and it’s partly due to demographic shifts in Japan where the population is eating more Western-style food.

Let Them Eat Herring

But some Bay Area chefs are interested in the plight of herring and they have an idea. It’s a counter-intuitive one. To save herring, they say, eat them.

“The solution is to eat herring,” says Kenny Belov, co-owner of Fish restaurant in Sausalito. “The solution is not to wipe out the population and ship it halfway across the world. We wouldn’t do any damage by leaving the fish in the Bay and taking less, higher quality, giving it to chefs that want to use the entire protein — from the roe to the filet to the bones. All of it.”

Belov says the notion of eating the local, seasonal fish is creating a buzz among area chefs. He explains chefs are pickling it, curing it, grilling it and serving it fresh. “And they’re getting their customers asking for it,” he says.

While the demand for herring in the Bay is still pretty low, the foodie plan might just reduce the pressure on an already stressed fish. Last year, local herring fishermen like Koepf got twice as much per pound for herring bound for local plates as for those headed to Japan.

Julian Bond and Michael Brune protest against Keystone XL Pipeline at Lafayette Park on Feb 13, 2013 in Washington, DC. (Photo: Leigh Vogel/Getty Images)

In the week leading up to Presidents' Day, Michael Brune, the national executive director of the Sierra Club, found himself in handcuffs, after strapping himself to the White House gates. He and other protesters are hoping to spur President Obama toward bold action to combat climate change with what's being billed as the biggest rally ever for climate action in this country. The Presidents' Day events in several cities, including San Francisco, where the Sierra Club is headquartered, mark a new, more aggressive stance for the organization spawned by John Muir. Brune's arrest was the first of a Sierra Club chief in the club's 120-year history.

Brune's not just rattling the gates from the outside, though. He managed to get sprung in time for the Valentine's Day roll-out of a major climate bill by Democratic Senators Barbara Boxer and Bernie Sanders. It would tax carbon emissions, tighten regulations on fracking and provide investments for clean energy and energy efficiency upgrades.

KQED Science Editor Craig Miller sat down with Brune before he left for Washington to talk with him about climate action, the Keystone XL pipeline, and fracking. This is an edited transcript of their conversation.

Craig Miller: Many people were stunned when the president devoted a full paragraph to the climate issue in his inaugural address. Were you among those stunned people up there?

Michael Brune: I was certainly very pleased. The president gave more word space to climate change than any other issue during his inauguration. He articulated both the moral obligation we have to fight climate change and the fact that when we transition to clean energy, there will be great economic benefit brought to all Americans. So it was very encouraging.

Miller: Surprising talk, but on the action front how would you grade this president so far? Have you been a little disappointed?

Brune: Looking at his first term, you can simultaneously say that the president did more than any other president when it comes to climate change, particularly if you look at all the rules that the EPA put forward to improve public health that had an impact on fossil fuels. You could say he has done an insufficient job in that there’s a lot of things the president could do and should do that he hasn’t yet done.

Miller: I think the reason a lot of people were surprised was the word climate just about disappeared from his vocabulary for an extended period of time.

Brune: Yeah, you know that’s disappointing. There’s really no other way to put it other than the fact that the president has the opportunity to lead not just the American people, but to lead the world in an all-out, concerted, thoughtful, but relentless effort to move away from dirty fuels and to embrace clean energy. He has to talk about climate every time that there’s another massive wildfire, or a crippling drought, or another super-storm hits. We have to be able to connect these extreme weather events to the fact that our climate is destabilizing as we speak. This is not something that can be addressed through the occasional mention or even the occasional rule put forward by his administration.

Miller: Do you think there’s been a sort of – no pun intended – sea change, a shift? Are people, are policymakers ready to see and hear what’s happening in your opinion?

Brune: I think so. I spend a fair amount of time on Capitol Hill and you can tell people’s opinions have shifted just in the last six months. The reason for that is the American public’s opinions have shifted. There was a poll put out last week by Duke University that said 84% of all Americans believe that climate change is real, it’s man-made, it’s happening and that the solutions to climate change are here. So you’re seeing that reflected in a thawing, let’s say, of some of the attitudes that we often see on Capitol Hill. The question remains is whether or not this will lead to meaningful action.

Miller: So what’s the most important first step that the president and Congress could take right now?

Brune: Job one is to reject the Keystone XL pipeline. We should not be building out new fossil fuel infrastructure at the same time we want to reduce greenhouse gas emissions.

Miller: This is the big pipeline that is designed to bring Canadian oil sands all the way down to the Gulf Coast for refining. There’s a lot of opposition to it, but here in California, it’s an issue that feels remote to a lot of people. Why does it matter to us out here?

Brune: There are two reasons why it matters. First is that this would be the biggest pipeline coming down from the tar sands. The tar sands is the dirtiest oil on the planet, and this pipeline would take 830,000 barrels of oil from the tar sands every day, bring it all the way through this country, and then have most of it be exported outside the U.S. borders. This will, by itself, contribute to global warming. But it’s also a symbol of the fact that we cannot continue to invest in dirty fuel sources whether it’s drilling in the Arctic, mountaintop removal in Appalachia, this tar sands project, fracking that’s happening across the country. We can’t continue to put billions of dollars of infrastructure into fossil fuels when we need to start investing that money toward clean energy solutions instead.

Miller: In fact, we’re waiting to hear from the president on (the Keystone XL project) issue. What if he approves it? What then?

Brune: We’re actually waiting to hear from the president on all of these issues. We’re waiting to hear from the president on how drilling should take place in the Arctic when we’re trying to reduce our dependence on fossil fuels. We’re waiting to see leadership from the president on the tar sands, as well. We’re waiting for a ruling that this pipeline should not be built. We’d like to see the president take on fracking as well as mountaintop removal.

The big rally on the National Mall was designed to inspire the president so that his ambition meets the scale of this challenge. We want to see the president reject the Keystone XL pipeline, but we want to see him go much farther than that. There’s an opportunity to regulate carbon pollution from smokestacks and refineries all across the country. There’s an opportunity to turn away from Arctic drilling and there’s an even bigger opportunity to invest in clean energy like solar and wind that will help to replace these dirty fuels. That creates more jobs and cuts air and water emissions at the same time.

Miller: Let’s talk about fracking. This is short for hydraulic fracturing the tech used to extract oil and gas from underground rock formations, stuff that was tough to get at before new technology made it possible. They’ve been fracking in California for oil in different ways but now it seems like there’s this new boom on its way here with the Monterey shale formation in Central California. How concerned are you about that?

Brune: As a parent, I’m very concerned about the impacts of fracking on our air, our water and our climate particularly when there are much better solutions to meet our energy needs, particularly in California, where we’ve got solar that’s just growing by leaps and bounds and wind resources that are not fully utilized. We know that in the 21st century our economy will be based on energy that’s safe, secure and sustainable. We don’t need to be investing in fracking, or more oil drilling, mountaintop removal or more coal mining when we know that solar and wind can do a better job.

Miller: But you can’t just throw a switch and tomorrow morning everything’s clean and renewable. In 2012, for example, U.S. greenhouse gas emissions fell to their lowest point in 20 years, and a lot of the credit for that is going to fracking for gas – cheap natural gas – which is cleaner than burning coal. Don’t you need to do some of that?

Brune: Let’s be really clear here. Greenhouse gas emissions have fallen to 20 year lows and the reason for that is not because of fracking — in no way, shape or form. The reason for that is we are replacing coal plants with a variety of clean energy sources. In most cases, wind and solar are taking up a bigger share of the energy mix than fracking ever is. Case in point, in 2012 there were more new wind resources brought online than natural gas. There was more solar and wind than all fossil fuel sources combined. What we are seeing right now is the United States slowly, but with increasing speed, is beginning to get off of fossil fuels — at a much slower pace than we should, but it’s starting to happen.

Miller: Going back to the D.C. rally, this kind of street-level activism is kind of a new direction for the Sierra Club, and it’s pretty much your doing since you took over. You must be getting some push back from some members who still see the primary mission of the Sierra Club as conservation of public lands and restoration of natural resources. Are you hearing some of that?

Brune: Not really. The mission of the Sierra Club is very simple. It’s to explore, enjoy and protect the planet. We have Sierra Club members who have been volunteering with us for decades, some members who have been volunteering for a couple weeks, but all of them are united around a very simple credo. We know that getting into the outdoors inspires further activism and we also know that there are solutions to some of our country’s biggest environmental problems. The demonstration on the National Mall over the weekend and the rallies we are holding across the country really does tap into a long-held tradition that Sierra Club members want to participate in bringing out solutions to our country’s problems, and they know there are a lot of ways to get there.

Miler: We had Jim Hansen here in the same studio for an interview recently – a certified climate change legend from NASA – who says that California’s whole approach is half-baked. We’d be much better off with a straight-on carbon tax than this complicated market-based cap-and-trade system that we’re using.

Brune: Hansen has a point. Most economists that you talk to will view a carbon tax as a much more efficient and, thus, much more effective way of putting a price on carbon and hastening a tradition toward clean energy resources. But it’s also true that California is making more progress than any other state in de-carbonizing and transitioning to clean energy.

Miller: Speaking of presidential decisions, Sally Jewell is Mr. Obama’s choice for the new Secretary of the Interior, currently the CEO of REI, the outdoor clothing and gear company out of Seattle. What specifically does Jewell bring to the table?

Brune: What Sally brings is potential for a sea change in terms of how the Department of Interior looks at natural resources. For the last century or more, most people who have been in her position have looked at the oil, or timber or gas as a resource to exploit. What Sally recognizes is that there’s more economic gain from protecting our public resources, but also there’s great opportunity to expand protection to benefit wildlife, landscapes and the communities that surround them. We’re very optimistic that when she assumes this position, we’ll have a great opportunity to get more people in the outdoors and then have those folks be active part in helping to protect our last remaining natural treasures.

A male northern elephant seal calling at Ano Nuevo State Reserve. (Photo: A. Friendlaender NMFS Permit No. 14636)

Love is in the air on California beaches this time of year, when northern elephant seals arrive by the thousands for breeding season. Males make plenty of noise at Ano Nuevo State Reserve, north of Santa Cruz, but it sounds more like a chorus of motorcycles than the melodious sounds of Barry White.

Now, researchers at the University of California Santa Cruz are decoding this complex communication system and learning how males use it to boost their reputation.

Elephant seals spend of the most the year alone in the Pacific Ocean, so there’s plenty of action packed into the two months they’re on land every winter. “That’s mating behavior,” says naturalist Lisa Wolfklain, pointing at two elephant seals in a sea of hundreds of males, females and pups.

Male elephant seals are the size of an SUV — fifteen feet long and 4,000 pounds. They’re known for their proboscis, the huge, fleshy nose that hangs over their mouth. There are plenty of available females this time of year, but most males will strike out. The dating scene is controlled by alpha males.

“The alpha strategy is to be dominant over a group of females, the harem," says Wolfklain. "And they want to have the first right to mate."

You can spot the alpha males right in the middle of their groups of 10 to 100 females. The other males, known as betas, are on the outskirts, just watching, waiting for their chance.

“So this guy's coming in,” says Wolfklain, pointing at one beta male moving quickly toward a female. The alpha male perks up and snorts a warning with customary bravado. Sometimes the fight ends there, but not this one.

“Ooh, now they’re hitting with their heads,” the commentary continues, as the two lunge at each others' chests. A few strikes seem to be enough for the beta male and he retreats.

These fights can be bloody and all the while, other males are taking advantage and sneaking in. It adds up to a very stressful time for male elephant seals.

It's All About Reputation

“It’s not advantageous for males to fight all the time,” says Caroline Casey, a researcher at the UC Santa Cruz. She says fights can be risky. “Sometimes they can result in death and we’ve seen that,” she says.

Elephant seals also don’t eat while on land, so they need to conserve energy. Casey says, as with humans, one way to avoid fighting is communication. But until now, no one was really sure what the males were saying to each other. So, she and her colleagues have been studying a patch of beach with about 50 males.

“We have come up with this ranking system where we assign each male a score,” she says. It’s similar to systems used in professional sports, where the males win or lose points with every fight. Casey and her team also recorded the males’ calls and found remarkable differences.

One beta male, X579, has a call that ends in a flourish. “His call, to me, is my favorite. He always has this really lovely note at the end of it,” she says.

X579 was a beta male with a lot of competition. “He tends to vocalize and challenge everybody right when he gets there,” Casey says. He challenged GL, an alpha male with a very short, staccato call.

“That is what’s so incredible. All of the animals sound completely different from one another,” Casey says. What’s more, Casey's team found that each male seems to use the same call year after year, whether he has a harem or not. It’s their signature call – and they flaunt it.

A female and pup at Ano Nuevo State Preserve. (Photo: Lauren Sommer/KQED)

“A larger, more dominant animal will come up to a smaller animal, maybe beat him up a little bit, call at him before and after, like, ‘Hey, this is me. I’m Bob. Don’t mess with me,'” says Casey.

It’s all about spreading your reputation around. “That’s called associative learning and that’s very unique among marine mammals, Casey explains. "That means that every male has the potential to be learning every other male based on their acoustic signature at that site."

These complex communication systems have been studied in songbirds and other animals, but Casey says less is known about marine species. “I think it’s just a piece of larger puzzle in understanding how these animals breed and how they’re going to survive.”

A century ago, elephant seals were hunted to near extinction for their blubber. Fewer than 100 lingered off the coast of Mexico. With protective laws in place, today there are 170,000 northern elephant seals and growing.

That’s good news for Casey’s loner elephant seal X579. This year, he’s an alpha male for the first time. As for the others, there’s always next year.

San Francisco pushed the shoreline of Ocean Beach up to 200 feet out into the ocean in some places. (Photo: Nicholas Christen/KQED)

Parts of New York and New Jersey are still reeling from Superstorm Sandy, an event that brought climate change and the threat of sea-level rise front-and-center. It's a looming problem for all coastal cities, and one that San Francisco has been pondering since long before Sandy struck.

Along San Francisco’s western shore, the Ocean Beach Master Plan [PDF] is a kind of test case for sea-rise planning. It calls for big changes, including a strategy known as managed retreat.

A taste of what's to come

You don’t need a crystal ball to see how encroaching seas will affect San Francisco.

"What we’re walking on right now is the former southbound lane of the Great Highway in San Francisco," says Tom Prete, the founder of the Ocean Beach Bulletin, an online news site that covers the neighborhoods along San Francisco’s Pacific shore.

"In the winter of 2010, the city closed this portion of Great Highway because of erosion that was endangering the road," he explains. The side of the road closest to the beach is now blocked off by concrete barriers. Traffic has been rerouted onto what was once the median, to avoid the receding sandy bluffs.

"It was something that was sort of done in an emergency," Prete says.

Now, rather than just reacting to what’s happening out here, San Francisco is planning ahead. The road map for this more proactive approach is the Ocean Beach Master Plan, a sweeping set of recommendations intended to be implemented over the next few decades as the ocean relentlessly carves away the coast.

"It wants this land back," Prete says. And it's taking it.

Man-made problems

Last year the National Academy of Sciences projected that in this part of California, sea level could rise nearly a foot by 2030. And by the end of the century, if current warming trends continue, it could be more than four feet higher.

Piles of boulders and rubble left from past attempts by the city to protect the Great Highway from erosion. (Molly Samuel/KQED)

Here at Ocean Beach, no private homes are in immediate danger, but on the line is millions of dollars’ worth of infrastructure: the four-lane highway and a waste water treatment plant. And there’s the beach itself, part of the Golden Gate National Recreation Area, used by surfers, dog-walkers, joggers and bundled up beach-goers (this is not San Diego).

Sea level rise is a looming threat, but erosion is nothing new.

"It's at least partially — I would argue, largely — a man-made problem," says Bob Battalio, a coastal engineer at the consulting firm ESA PWA who is working on the Master Plan. He says the Great Highway isn’t just a casualty here; it’s part of the problem.

It opened in 1929 to much fanfare. But it wasn’t exactly built on Terra Firma: the city flattened coastal sand dunes and pushed the shoreline about 200 feet out into the ocean.

"It was progress I guess at that point," reflects Battalio.

But the ocean has been pushing back ever since and the Great Highway isn’t looking so great anymore, with pieces of parking lots crumbling onto the beach. The bluffs below it are strewn with sandbags, boulders and concrete: failed attempts by the city to stem erosion.

Climate change will make it all worse.

"It’s kind of like trying to hold a pendulum, and it's going to try to go back to where it wants to be," says Battalio. "Otherwise you have to hold it there."

Retreating from the rising tide

The most dramatic recommendation in the Ocean Beach Master Plan is to let go of the pendulum.

Ocean Beach hasn't always been where it is now. Click on the map to see more information about past shorelines. (Map courtesy of Elena Vandebroek and Bob Battalio, ESA PWA)

"Everything's easier if you move back," Battalio explains. "So ultimately what we’re trying to do is what we call 'managed retreat.'"

Under the plan, San Francisco would close one end of the Great Highway, reroute traffic about a half-mile inland, and let the ocean come back. Battalio says it comes down to engineering and economics.

"As a surfer and somebody who’s studied waves and the like, I think it’s fine if people want to live on the coast," he says. "But I don’t think it’s okay to take public money and build structures that adversely affect the beach. I don’t want my money going there."

For years surfers have been asking San Francisco to manage the erosion problems at the south end of Ocean Beach. (Photo: Sean Greene/KQED)

Translating high-concept plans to work on the ground

The plan would cut down on those kinds of costs, but it isn't cheap, either. Estimates for completing all the recommendations are just north of $350 million. Funding has come through for some initial studies, but the vast majority of that money has yet to be raised.

"A lot of the things we're recommending at Ocean Beach are very expensive," says Benjamin Grant, who manages the Ocean Beach Master Plan for the San Francisco Planning and Urban Research Association (SPUR). "But you have to set them against the costs of the band-aid measures already taking place."

SPUR is acting as a facilitator for the project, bringing together the myriad city, state, and federal organizations involved.

"We can't close our eyes to what’s coming and it’s definitely going to get worse and not better," Grant says. "If we can find a way to work with those processes to achieve the kinds of outcomes and build the kinds of places we want to have in our city, then we’ll be ahead of the game."

Two other California cities, Pacifica and Ventura, have both undertaken smaller managed-retreat projects. And other places, including New York City and the states around Chesapeake Bay, are beginning to put together their own climate response plans.

For San Francisco, completing the big vision of the Ocean Beach Master Plan is just a first step. Some traffic and engineering studies are underway now, but they’re just the beginning of a decades-long process that will affect the shape of our coast and the lives along it.

The plan also will be closely watched by other coastal cities around the United States, as the sea continues its slow but steady rise.

Green Engineering Academy students with the engineering teacher. (from left to right) Priya Sri-Tharan, County engineer Puck Ananta, Areli Hernandez, Laila Hassen and Natasha Moore. (Photo: Rachel Dornhelm/KQED)

President Obama raised eyebrows earlier this month by elevating climate change to a top national priority in his inaugural address.

California has long been a policy leader on the issue. In the last election, voters overwhelmingly passed Proposition 39, which closed a corporate tax loophole and uses the cash to create the largest energy-efficiency initiative of any state.

The proposition requires the money be spent on public buildings, however the details have been left to lawmakers. Now there’s the predictable debate over who will get the money and how it might be spent.

Can I audit this class?

Tour Livermore High School with some students from the Green Engineering Academy and you’ll hear plenty of suggestions for energy efficiency upgrades at their school.

“What would be nice is if they had skylights,” says senior Natasha Moore. “So more natural lighting can come in.”

Senior Laila Hassen says the benefits go beyond cost savings.

“They've shown that when students are under hours of fluorescent lighting they can’t concentrate as well” she says. “It can actually hurt their eyes.”

Moore and Hassen are part of the Leadership in Energy Efficiency Program, or LEEP. The program is funded by Pacific Gas & Electric Corp. and administered by the Alameda County of Education. These students completed a district-wide energy audit with the help of an engineering firm, saving the school thousands of dollars.

On tour, the students point out a new motion sensor attached to an old snack machine, that keeps the lights and cooler from running idly. But the students want to do better. They want the latest energy efficient machine.

Junior Priya Sri-Tharan says it would almost pay for itself the first year with $2,000 in energy savings.

“If you turn down the little stuff,” says Sri-Thran. “It’s going to eventually add up.”

Susan Kinder, the chief business official for Livermore’s school district, agrees.

“We’ve been saving between 15-and-20 percent of our electricity bills already,” says Kinder, “just with the small changes we’ve done so far.”

That’s about $300,000 a year. Kinder says she’d like to do more. But in a tight funding environment where their current energy savings are going to keep basic programs afloat, where does one find the initial investment?

“That is the huge hurdle,” says Kinder.

A billion-dollar windfall

Enter the windfall from Proposition 39, almost single-handedly bankrolled by San Francisco hedge fund billionaire Tom Steyer. California voters approved the November, 2012 initiative by a nearly two-thirds margin.

The measure will raise an estimated $1.1 billion a year from the closed tax loophole. Half will go directly into the state general fund. But for the first five years, the other half will be used to retrofit public schools or public office buildings.

“When you come up with half of a billion in one year,” says Steyer, “a lot of people put out their hand and say, 'I have the exact solution for you.'”

Steyer says one of the goals is to create tens of thousands of construction jobs.

“It would also be an investment,” says Steyer. “So that in spending this money we would save money for the next 25 years because we would have reduced energy bills.”

Altogether, the measure is expected to generate $2.75 billion in new money by 2018 for energy efficiency projects. Experts project the money could fund efficiency upgrades at half of California’s public schools, shaving 20-to-40 percent off their monthly utility bills.

Some people want to spend the Prop 39 money on basic upgrades like new windows, others are advocating for renewable energy installations like solar panels. (Photo: Craig Miller/KQED)

Competing needs

So who should get the grants? Governor Jerry Brown’s proposed budget has it spread around all public schools. But State Senator Kevin De Leon, a Los Angeles Democrat, has introduced legislation to distribute the money based on need.

“Every school district is different,” says De Leon. “You have some districts that have brand new schools, and within the same district you have schools that are very old, schools that emit a lot of carbon and waste energy."

Take Fremont High. The Alameda County school is slated for a rebuild. On a recent visit here, the school had been dealing with a broken boiler line. Space heaters dotted the hallways.

Just across the county, Albany High School stands in contrast. Eight years ago the district worked to do basic school retrofits like lighting, as well as investing in a technology uniquely suited for their high school: a co-generator. It creates electricity for the school while producing heat for the two pools.

Albany Unified Superintendent Marla Stephenson says the carefully tailored investment paid off and the district has, “saved at least $100,000 a year.”

“It started with cost,” says Stephenson, “and it’s now moved to what’s good for the environment and global warming.”

Yvonne Tom oversees energy efficiency programs for the Alameda County Office of Education. She says in her years working on a variety of campuses, she's learned a few lessons she would pass on to lawmakers.

“We need really good quality audits done by a real engineering firm,” says Tom, “who has not a vested interest in selling you a particular product.”

Tom advocates spending some of the Prop 39 money to hire experts at a county level to help districts make the best use of funds.

Others advocate spending on “the low hanging fruit,” basic energy efficiency upgrades, like new windows and lighting. Senator De Leon says these provide the most savings for the least cost.

Adam Browning, with the non-profit group Vote Solar, argues for renewable energy systems like solar panels. Browning says the ballot measure explicitly included clean energy solutions in its language and that should guide implementation. Anything else, he says, “reeks of a bait and switch.”

“They didn’t just show pictures of compact fluorescents,” says Browning. “There were plenty of solar panels that were used to sell this and voters expressed their preference for something. They had it before them. That should be honored.”

The state Legislature is expected to pass a plan to distribute the money later this summer.

It's not the frenzy of 1849, but gold mining is quietly making a comeback in California. A soaring gold price is drawing miners back into the Sierra Nevada foothills, in some cases, to the very spots exploited by the original 49ers.

Not everyone is happy to see gold mining return. While some communities are concerned about the environmental costs, others see the chance for a "greener" gold rush this time around.

Miners today, as during the Gold Rush were searching for veins of white quartz with gold inside. (Photo: Lauren Sommer/KQED)

The return is being heralded in Sutter Creek, about 45 miles southeast of Sacramento. Just a few years ago, local resident Dan Boitano was a tour guide there. He led tourists into the empty, underground Lincoln Project Mine. In the late 1840s, miners flooded into these foothills when gold was discovered nearby.

“I’m actually a fifth generation miner in the area,” Boitano says. “My family came here for the Gold Rush.”

Boitano still works in this mine, but now, he’s mining. Hundreds of feet below ground, in a narrow tunnel, two of his colleagues drill into a solid face of rock. Matt Collins, chief operating officer of Sutter Gold Mining, Inc., looks on.

“This is December’s gold production right here in the palm of my hand,” Collins says, holding out a half an ounce of gold. “This is the first of what we hope will be many, many, many ounces of gold.”

Sutter managers hope to produce almost $200 million in gold over the next five years. The company is just starting full-scale production in this web of burrows – tunnels that only get darker and narrower the deeper we go.

“Remember when they first started mining here, they would have been mining with candles,” Collins says.

Miner Steve Ator outside the Lincoln Project Mine in Sutter Creek. (Photo: Lauren Sommer/KQED)

Mining was treacherous work for the original 49ers. They used hammers and dynamite in search of what’s just above my head: a vein of white quartz rock with dots of gold. “This one runs for many hundreds of feet,” Collins says.

This is a slice of the Mother Lode – the most legendary gold deposit in the state. There are two dozen old mines within ten miles of this one. They produced millions of ounces of gold up until World War II, when work was suspended for the war effort.

“After having let the mines flood, the timbers rot, the neglect and the lack of maintenance, it became very expensive to reopen the mines,” says Collins.

The Mother Lode still holds plenty of gold and with gold prices having steadily risen to around $1,700 dollars an ounce, reopening old mines has become tempting, but not necessarily easy.

“California is burdensome. I would say this is one of the toughest regulatory climates there is on the planet,” Collins says.

Some of the Golden State's strict environmental laws spring from the legacy of environmental damage that mining has left behind. Early miners processed gold with toxic mercury, dumping millions of pounds of it into the watershed. Even today, some fish aren’t safe to eat as far downstream as San Francisco Bay.

“Today we have to have a much different approach. We have come into a project like this thinking about these potential impacts,” Collins says.

Those potential impacts are a big issue in another community where a local gold mine is trying to reopen. About two hours north in Nevada City, the San Juan Ridge Mine originally tried to get going in the 1990s, but things didn’t go so well.

“My wells right around us here in the north Columbia area started to go dry,” says local resident Kurt Lorenz.

The mine had hit an underground formation full of water. As workers pumped the water out, 14 neighborhood wells dried up. The mine paid for deeper wells to be drilled, but Lorenz says the new wells had poor water quality. The local school, Grizzly Hill Elementary, was told it couldn’t drink the water.

“The solution was the mine started paying for bottled water to be delivered to the school,” Lorenz says.

The mine put in a water treatment plant but Lorenz, who was on the school board at the time, says it was years before the school was using tap water again. In the end, the mine shut down because of the added costs and flagging gold prices.

Now, the issue is surfacing again because the mine wants to reopen. “We don’t want a repeat of what’s happened in the past,” says the schools current principal, James Berardi. “We can’t take that chance. We don’t want to do it again.”

“I don’t expect the community to take any significant risks for the benefit of my operation,” says Tim Callaway, CEO of San Juan Mining Corporation. He says the risks are lower this time because the mine will use better surveying and engineering.

Callaway knows it’s a tough sell in this community, but points to the economy. “What this project offers is really high-paying jobs,” he says. “There are very, very few industries or jobs in rural communities.” The decision will ultimately be up to Nevada County, which is doing an environmental review.

All of this adds up to an interesting moment for gold in California, says Izzy Martin of the non-profit Sierra Fund. There are environmental risks, she says, because not all counties are equipped to do thorough reviews of proposed mines.

But Martin also sees an opportunity. “Gold mining around the world is heart-breaking to think about,” she says. “People use really toxic chemicals. There’s no doubt that if we could open a mine in California that met our environmental quality act standards, our clean water acts standards, it would be the cleanest, greenest gold in the world.”

Martin wants to see "green" gold standards set up in California that would enable consumer labeling. Responsible mining, she says, has the potential to give gold an entirely new legacy in the state. A handful of other proposed mines are hoping to join that legacy.

New Bullards Bar Dam in Yuba County is the fifth-highest dam in the United States. (Photo: Molly Samuel/KQED)

There are more than 130 hydropower projects in California. They take advantage of steep terrain and gushing mountain rivers to churn out about fourteen percent of California's electricity.

It's a delicate balance, dependent on heavy snow in the winter, and heavy runoff in the spring as the snow melts. But climate change threatens to throw that balance out of whack, a problem that federal regulators have chosen to ignore.

A High-Stakes Game

New Bullards Bar Dam stretches across a steep rocky canyon in the Sierra Nevada foothills, about fifty miles northeast of Sacramento. It's the fifth-highest dam in North America, towering more than sixty stories over the North Yuba River.

"I get to run around to all these glorious sites, and work on a multitude of issues," says Geoff Rabone. He works for the Yuba County Water Agency, which owns this and other smaller dams, plus a network of reservoirs, water diversion tunnels and hydroelectric facilities. Standing on top of the spillway, we can see vultures circling below us.

Rabone manages relicensing for the water agency. Every few decades, hydropower projects have to get a new license from the Federal Energy Regulatory Commission, or FERC. If you think going to the DMV is bad, be glad you're not a dam. Applying for a new hydropower license takes years and costs millions of dollars. It seems like everything gets considered, from how the dams affect water supply, to endangered species, to whitewater sports.

"We have 44 different studies going on right now," Rabone tells me.

In the end, the new license will dictate how much electricity the project generates, and how much water it releases — and when — for the next thirty-to-fifty years. That's why there are so many studies, and why FERC relicensing is so important to water agencies, power companies and environmental groups, among others.

But there's one looming issue that Rabone doesn't have to wrangle any studies for: climate change. FERC doesn't require those.

Climate Change and the "New Normal"

"It's an approach akin to the cliche of putting their heads in the sand," says Steve Rothert, the California director for the environmental organization American Rivers. Rothert says he has asked FERC to include climate change in the relicensing process, but they've turned him down.

Climate change projections for the Sierra Nevada vary. The region may get wetter; it may get drier. But scientists agree that it will get warmer, dramatically affecting the snow where most of the region’s water comes from– and not just in the distant future. There’s evidence that we’re already seeing effects of climate change in the Sierra.

"And yet the power companies and the Federal Energy Regulatory Commission refuse to consider how climate change will affect these dams and these rivers for the next 50 years," says Rothert.

PG&E's Belden Powerhouse is part of the chain of hydro facilities on the Feather River, known as the "Stairway of Power." (Photo: Craig Miller)

Josh Viers, an ecologist at The University of California – Davis, is similarly perplexed. He argues that FERC's decision to depend only on historic weather and water records doesn't make sense anymore, especially for licenses that won’t expire for decades.

"Most of the projections for California in particular — and these are multiple scientists using different models and different assumptions — all converge on the same idea," explains Viers. "The climate 35 years from now is not likely to be what we see today."

One recent study suggests the emergence of a “new normal” within the next few decades, one in which eight-in-ten winters in the western U.S. will see snow accumulation below what we now consider normal.

Viers says the way California manages water will have to change. Right now, the snowpack itself serves as a reservoir. If it melts earlier, or if more precipitation falls as rain, our man-made reservoirs may have to spill the extra runoff, which could mean more floods in the winter, and more water shortages in the summer.

"We have a lot at stake," says Viers. "So it seems it would be in the public’s best interest if in fact FERC were looking out for the public."

In fact, the strategic planner for one Sierra utility says, when his agency included an entire section on climate effects in its relicensing application, FERC didn’t want it.

Why Not Consider Climate?

FERC officials acknowledge that climate change will have an impact on hydropower, but say the climate models scientists have developed just aren't specific enough to project local impacts.

"There are not really any models yet that are granular enough that we would feel comfortable basing a decision on the impact of climate change on an individual facility," FERC commissioner John Norris told me.

FERC has also said that the focus of relicensing studies is on how hydropower operations affect resources, not how other things — in this case, climate change — affect them. Rothert of American Rivers says that's a red herring, though; the studies he's asked for would concern how hydropower projects affect resources in a changed climate.

If federal regulators are "whistling in the dark," Rabone from the Yuba County Water Agency says climate change is very much on his mind.

"It's going to be very interesting to see what happens, if climate change turns out the way it's theorized to work out," he says.

If it does, the job of water managers — balancing the needs of fish, farmers and power plants — will only get more complicated as the climate changes, whether or not regulators are paying attention.

Stanford vs. UCLA. Photo: Ezra Shaw/Getty Images

It's no secret that concussions are endemic in American football at every level, from pewees to the pros, but little is known about the hits that cause them. Stanford University is searching for answers by meticulously gathering data on every impact their football players sustain. The study is only in it's second year, but they've already made some interesting discoveries.

David Camarillo is a bio-engineer at Stanford and a lead researcher on the project. He says “injury research is a tough thing to do because you usually see it only after it happens.” To see brain trauma in real time, Camarillo and his team have outfitted the football team with mouth guards that measure the physics of every hit. At practices, they use ultra-high-definition, slow-motion cameras to observe those collisions more closely and look for ways to prevent them.

Mouth Guards with sensors

The first startling discovery of the research is how little is known about the “injury mechanism” for concussions, that is, exactly how they are caused. People have long associated “getting your bell rung” with a hard hit, or a series of repeated impacts, but little data has been gathered on the nature of those hits. How hard does a hit need to be to cause a concussion outright? How many small, low-impact hits before a player begins to exhibit concussion symptoms?

The definition of a concussion is a fairly simple one: the damage caused when the brain smashes against the inside of the skull. They can come from one hard impact, or repeated low-speed hits. In the short term they cause things like dizziness and loss of memory; in the long-term they can cause severe neurodegeneration. But the diagnosis process for concussions is complex. Symptoms vary widely from player to player and can be easily lied about.

Scott Anderson is the head athletic trainer at Stanford and he's helping to develop the mouth guard prototypes. He says right now there's no good way to analyze and diagnose concussions. With an injury like a sprained ankle or broken rib, a physician can use an MRI or an X-ray to look at the problem. With a concussion there's no way to peer inside the brain and see what's going on. “We can send you for a CT scan to look at your brain,” he says, “but your brain doesn't show us anything.” Instead, physicians have to rely on players to describe symptoms, and players can be highly unreliable.

In a recent survey by Sporting News, more than half the players polled said they would hide symptoms to keep playing, and for good reason. A concussion can cost you your starting spot or, in the case of Greg McElroy of the Jets, your moment to shine .

Alex Smith of the 49ers learned the job-threatening implications of a concussion the hard way. When a concussion sidelined him earlier this season, the replacement quarterback Colin Kaepernick played well and took over his starting role. Now Kaepernick is flourishing while Smith watches from the bench.

With the mouth guards there's no hiding or lying about hits. The team wears the mouth guards at all games and practices so that researchers can generate a comprehensive database of every impact they sustain. The sensors measure linear and angular acceleration—how fast the head is moving in one direction and rotating. The sensors may sound high tech, but actually, you might have some in your pocket right now. They are the same ones used in the iPhone 5.

Camarillo says the mouth guards have already captured some startlingly hard hits, like the one that ended the season for a wide receiver. That collision registered an acceleration of 150 Gs, that's 150 times the acceleration gravity. “Pretty serious business,” he says, “a standard boxing punch is probably between 10-20 Gs.

That's just acceleration in one direction. The player's head was also spinning at 2000 degrees per second—which means his head would have rotated five and a half times in one second if it weren't anchored to the neck. While it has long been suspected that this kind of angular acceleration plays a role in concussions, Camarillo says no one has gathered data on it. What's more disturbing is that angular acceleration has been completely ignored when it comes to football safety measures.

The standard industry lab test for helmets is basically a plunger that smashes a helmet down onto a hard surface. The test hasn't changed much since it was first developed back in 1973 by NOCSAE, The National Operating Committee on Standards for Athletic Equipment. The test doesn't account for angular acceleration at all. “The device,” Camarillo says, “doesn't have any kind of neck.”

A number of research groups are conducting similar studies by putting sensors in the helmets but athletic trainer Anderson argues that the mouth guards give more accurate results. He says the initial data has already revealed something new. Some hits they used to consider as just one are actually two successive collisions. The player has an initial impact during a tackle but the brain receives trauma again when the head collides with the ground. Anderson says the double hit is generating more concussion impacts than a single hit.

Senior fullback Ryan Hewitt

For the freshmen players, Camarillo and his fellow researchers will be able to gather five years of data. He doesn't expect players at Stanford to have long-term damages if they just play at the collegiate level. But if brain problems begin to show up years down the road, the research team will have accurate records of the impacts they received playing college football.

The success of this study relies on a collaborative effort with a number of different departments at Stanford. Anderson says it's an unprecedented time of cooperation between the sports department, various research groups, and the players. Senior Fullback Ryan Hewitt says he's happy to be part of the study, even though he and his fellow players are “sort of the guinea pigs.” “I figure we might as well use someone,” he says, “and why not use us.” Hewitt hopes the data will help researchers figure out a little more about why concussions happen and eventually develop ways to prevent them.

Camarillo says it's going to take a long time to get any answers to those questions. Even with a big pool of data, he thinks it will be five to ten years before they can even begin to crack what causes concussions.

* The US Senate has organized a committee to conduct an in-depth study on sports-related concussions. They will be having their first meeting on Monday, January 7th.

This story originally aired on January 6, 2012.

It's that time of year when we let go of the old and bring in the new. And that often means setting New Year's resolutions. Some are able to keep to their new goals but most of us eventually just give up. Changing behavior is no easy task, but one Stanford professor has developed a new technique. He says not to worry about New Year’s goals. Instead, we should focus on “tiny habits.”

What’s a tiny habit? Fogg demonstrates by picking up his ukulele and playing for 30 seconds. "I used to play ukulele a lot. But I stopped practicing for a while so to get back into it I thought I’m going to create a tiny habit of just practicing this cord sequence," he says.

“I set it right by the piano so right after I finish breakfast I go pick the ukulele up. That’s what a tiny habit is. It’s a very little thing that you sequence into your life in a place that makes sense and you work to make it automatic.”

Thirty seconds doesn’t seem like much when you compare it to goals like getting in shape or eating better. But these broad ideas are where Fogg says most people get into trouble.

Resolutions vs. Habits

“What a mistake – the whole idea around New Year’s resolutions. People aren’t picking specific behaviors, they’re picking abstractions,” he says.

Abstract goals don’t work, says Fogg, when they aren’t tied to specific behaviors. And to retain new behavior, he says it needs to be instinctual. The more you have to remember to do something, the better the chances are that you’ll talk yourself out of it.

“The strength of a habit is defined, at least the way I see it, is how much of a decision was that behavior. So if you’re deciding ‘yeah, I’m going to go to the gym today’ it’s a pretty good indication it’s not a habit. Habits are things you do without deciding,” says Fogg.

Classic behavior models focus on decision-making as a key component of behavior. Fogg is trying to get away from that by working on a new model of habit formation that’s built on baby steps.

Forming a Habit

Take something like flossing your teeth. Instead of trying to floss all your teeth every day, Fogg says start with flossing just one tooth.

Next, find a habit you already have and do your new habit immediately after. “For me and for most people, brushing your teeth is a solid habit. So that can serve as a trigger for the new behavior you want.”

Then, reward yourself. “You declare victory. Like I am so awesome, I just flossed one tooth. And I know it sounds ridiculous. But I believe that when you reinforce yourself like that, your brain will say yeah, awesome, let’s do that.”

And once the habit is formed, Fogg says you’ll find yourself flossing all your teeth. That’s a theory he’s testing out, at least, with several hundred volunteers. Fogg put out a call on twitter, asking participants to do three tiny habits for a week.

Testing the Model

One of those people is Charles Wang, a psychiatrist in Palo Alto, who picked flossing as one of his habits. “So right now I’m probably doing on average six or seven teeth, I think,” he says.

He’s also trying to do ten pushups as soon as he wakes up and to answer emails as soon as he opens them. “When I look at the email, then I just say, you know, I’m going to immediately hit reply and then send a response. There are still times where it’s just challenging to do that one so I don’t always do it.”

If the ideas of behavioral triggers and rewards sound familiar to pet owners, Fogg says there’s a reason. “If you really took the techniques for training dogs and applied it to yourself, you would have much better success. Now, I’m sure people are upset with me for saying that because people want to think we’re different from other animals. When it comes to behavior, we’re a lot more alike than people want to believe.”

Fogg is eager to see if a person’s habit-making ability improves with every new one they make. And he believes understanding habit formation better is vital to industries like medicine and healthcare.

“The mistakes that are being made are pretty predictable. Don’t create a system that assumes that people are going to make these big huge changes in their lives. The good news is there are a lot of things in the works to help people stay healthy.”

An oil field in Kern County. Regulators says fracking has been used in California for five decades. (Photo: Craig Miller/KQED)

The controversial drilling technique known as hydraulic fracturing has created an oil and gas boom around the country – and that’s left state governments grappling with how to regulate it.

Now, California is wading into that fight. State regulators are expected to release California’s first rules on fracking by the end of the month.

Hydraulic fracturing has revived oil and gas development in places like West Texas. Thirty years ago, the oil industry there went bust. Now, it’s booming.

“We don’t do things the way we used to do them,” says Ben Shepperd, president of the Permian Basin Petroleum Association, a regional trade group in West Texas. He’s standing next to a towering rig that’s drilling a new oil well on the outskirts of Midland.

“In the 20s, a frack job was: once you drill a hole, you drop TNT down the hole and crack the rock that way. That was an old-fashioned frack job.”

Fracking technology has come a long way since then. Oil companies drill horizontally underground along a layer of oil-saturated shale rock. Then, they inject water mixed with sand and chemicals into the well at high pressure. That cracks the rock, releasing the oil inside.

Shepperd says companies are spending a billion dollars a month on drilling in West Texas. But that activity has brought new attention and new rules on things like the spacing of wells.

“The city of Midland updated their drilling ordinance to require setback distances and to require notification of landowners,” he says.

Around the country, regulating fracking has been largely up to state, county and even city governments. In places where hundreds of new wells have gone in like Pennsylvania, Colorado, and New York, the battles have gotten ugly.

“I think we were late to this game,” says Bill Allayaud of the non-profit Environmental Working Group. He says just a few years ago, it wasn’t clear if fracking was widespread in California. So, he asked state regulators.

“They said we don’t need to frack here. We don’t need to get gas out of the ground that way. But it turns out we’ve been getting oil out of the ground that way for decades,” he says.

California’s Division of Oil, Gas and Geothermal Resources (DOGGR) confirms that fracking has been used in the state for 50 years. The agency doesn’t require drillers to specifically report fracking, so it couldn’t say where it’s been happening.

That began to worry Allyaud as issues emerged around the country. “There’ve been well blowouts, there’s been spills into water bodies, there’s been contamination of groundwater,” he says. There have also been reports of health effects. But in most cases, the studies haven’t been conclusive on whether fracking was responsible.

“Maybe some is true, maybe some isn’t. But we’re pretty sure there’s enough solid evidence now to ask more questions, to get better scrutiny, to make sure here in California that we’re up to the task,” says Allayaud.

The Environmental Working Group and others co-sponsored a bill in the state legislature that would have required more disclosure about fracking. It failed two years in a row – amid opposition from the oil industry.

Now, state regulators are stepping in. They’re drafting fracking regulations for the first time.

Upcoming Draft Regulations

“We’ve heard this often – this was an unregulated activity,” says Tupper Hull, a lobbyist with the Western States Petroleum Association.

“That’s a statement that we strongly disagree with. This is a state where industrial activities and certainly oil and gas activities are heavily regulated.”

But because of the new attention, Hull says many oil companies are now voluntarily reporting where they’re fracking on the FracFocus website.

“We recognize that there’s a desire on the part of a lot of people to see disclosure and we fully expect that we will be required to disclose the chemicals that are used in hydraulic fracture, the location of hydraulic fracturing,” Hull says.

“What these regulations are focusing on is really to make sure the operators are pre-planning the frack job to make sure it’s done correctly, monitoring during fracking and reporting after,” says Tim Kustic of DOGGR.

“A lot of this has already been going on, It just hasn’t been captured in regulations. It’s just industry’s best practice,” he says.

Drilling site in West Texas, where hydraulic fracturing has led to an oil development boom. (Photo: Craig Miller/KQED)

Kustic says the regulations probably won’t make drillers disclose the precise chemical recipe of their fracking fluids, since it's considered a trade secret. And when it comes to monitoring groundwater around fracking sites to detect contamination, Kustic says that will likely be left to the State Water Resources Control Board.

Then there’s California’s complex geology. “You don’t want to be hydraulically fracturing an active fault,” says Mark Zoback, a geophysicist at Stanford University.

He says the likelihood that fracking would cause a big earthquake is relatively low. But there could be an issue with the fracking waste water. Drillers often dispose of it by injecting it in underground wells, which builds up pressure.

“It takes a big fault to make a big earthquake. And it’s sort of a no-brainer – you don’t inject into existing faults, especially big ones,” Zoback says.

State regulators aren’t likely to deal with that in the fracking regulations, but Zoback says it’s something they’ll have to pay attention to.

“You know it’s not hydraulic fracturing is good or hydraulic fracturing is bad. Hydraulic fracturing is safe or hydraulic fracturing is unsafe. On a case by case basis, you have to consider what’s safe to do and what’s not.”

State regulators hope to finalize California’s first fracking regulations sometime next year.

Workers at the Marcellus Shale in Pennsylvania. (MLADEN ANTONOV/AFP/Getty Images)

California regulators are expected to release new fracking regulations by the end of the year. The state doesn't currently have fracking-specific rules, but some activity falls under the state's oil and gas regulations. Nationwide, regulations differ from state to state.

I spoke with Nathan Richardson who is a resident scholar at Resources for the Future, a policy and economics think tank in Washington, D.C. to learn how California's current oil and gas rules compare to other states'. He’s working on a survey of state fracking regulations around the country. You can explore a map comparing states on different issues at RFF’s website.

This is an edited version of the interview.

How do California’s current regulations compare to other states’?
Our survey is about fracking for shale gas and the majority of fracking occurring in California is for shale oil. But I think it’s still useful to talk about the shale gas regulations in California because a lot of these regulations apply to the process of getting oil and gas from the ground, not fracking in particular.

California’s regulations on shale gas are relatively unexceptional. If I wanted to pick out some things where California’s regulations are a little bit different from other states, one thing is that California relies somewhat heavily on its permit process. For casing and cementing in wells, for example, California jumps out as a state that uses a case-by-case approach, as opposed to a uniform statewide standard about how to case and cement a well.

One other thing I noticed is when a well is shut down, you don’t want a bunch of idle wells out there because those can cause risks. So states limit the amount of time a well can stay idle. California does limit this amount of time, but the length is among the highest in the country; it's 300 months. It doesn’t necessarily imply that’s the wrong balance to strike, but it is something California does do differently than most other states.

Let’s go through some of the big issues when it comes to regulating fracking. The first is what chemicals companies are using in their fracking fluid. How are states handling disclosure?
One area where there’s kind of an emerging trend in one direction is with frack fluid disclosure. Not every state that has any shale gas operations requires fluid disclosure, and those states that do require it don’t always require the same thing. Some of the laws that are being passed in diff states are pretty similar,  although they have different exceptions for things like trade secrets.

But there’s a lot of similarity here and it really seems like even in the past couple years the trend has been towards disclosure of these fracking fluids to the public. Part of that’s because either opponents of shale gas or proponents of more regulation for shale gas have really made this an issue that they’ve pushed hard. Also the industry has gotten on board: in a lot of states they’ve realized it’s in their interest to be open about what they’re doing, to help them back up their arguments that this activity is safe. So a consensus has developed around fluid disclosure.

How do different states deal with wastewater?
Wastewater is complicated. In contrast to what I just talked about with fluid disclosure, this is one of the areas where states have great differences in what they do. There’s different things you can do with the wastewater. You can recycle it, you can inject it under ground, with certain kinds of wastewater you can store it in pits until it evaporates, with some kinds you can even use it in the winter to keep snow and ice off your roadways. There’s a lot of different kinds of fluid that come out of the ground depending on the geological formation and the condition of the well, and local conditions are different.

All of this results in a lot of difference among states and how they regulate this. All states allow fluid to be recycled. Many states allow it to be injected underground, but there are a few states that specifically disallow this, in a lot of cases because of fears that this will cause earthquakes.

What about setback rules? It looks from your maps that there is a range from a couple hundred feet to a couple thousand feet.
Set back restrictions essentially say that you must drill a well at least a certain distance away from something else. That something can be a building, a church or a school, a source of water, a source of drinkable water.

This is an interesting story because at the 10,000 foot level, states look the same. But states have different rules about what wells have to be set back from, and how far they have to be set back. States in the west where there just isn’t as much water may be worried about water impacts, while places in the east which are more densely populated but richer in water are more worried about impacts on people and communities. You see some of that reflected in the regulations, but I’d hesitate to call it a trend.

And what about monitoring for water contamination?
A few states have regulations that require the developer to test or to pay for testing of local water wells or local water sources before they frack. There are not many states that require this — only 7 or 8 of them. California does not require this right now as best as we can tell.

The reason to do this is, if some problem does occur later, and the driller wants to say, “No that problem was already there, it’s not us,” it allows the state or the landowner to say, “Well let’s go back and check the data and see if you’re right.”

If this data isn’t available it makes attributing any contamination that is uncovered later really hard. So there’s some fairly strong arguments for having this pre-drilling testing, but it’s not free and there are also a lot of states that don’t really depend on well water as much so it may or may not make sense to have testing in that state. Even the states that do have testing, the distance away from the well that needs to be tested really varies a lot too.

What role does the federal government play?
The states are the real show here. States are the ones that are on the ground doing the vast majority of regulation, not only of shale gas development, but oil and gas entirely. The entire history of oil and gas has been almost exclusively a state-regulatory activity. Some people don't like that. A lot of greens think the feds should do it. The industry really likes the states doing it.

The federal government has always had a role in protecting surface water. The Clean Water Act gives a lot of power to regulate what can and can't be put into rivers and water in the United States. Putting oil and gas waste into water is almost uniformly illegal, and the reason it's illegal is because the federal government prevents it from being done.

Air pollution is traditionally a federal area. It's regulated primarily under the Clean Air Act. The EPA passed performance standards, that required oil and gas operations to reduce their emissions of Volatile Organic Compounds, and required them to use processes called "Green Completion" that reduce the emission of all kinds of air pollutants, including methane, which is a powerful greenhouse gas.

There is one other layer that is worth mentioning, and it's especially relevant in the West. The federal government is not just a regulator; it's also a huge land owner. And to the extent that the federal government limits what can be done on the lands that it owns, it's really acting as a landowner. Just like if you and I own a piece of property, and a driller wanted to drill there, we could say, "Yeah, you can do that, but you've gotta use these super safe practices," or, "You can do this and not that." The federal government can do that, and the Department of Interior does issue rules about what can and can't be done on its land. It’s just that that starts to look like a regulation when you're in a place like Nevada or Utah, where the federal government owns most of the state.

Vineyards in Southern Monterey County.

The new oil-and-gas boom that’s sweeping the country may be coming to California. With it comes the controversy over the drilling technique known as hydraulic fracturing – or fracking. Widespread fracking in other states has launched a national debate over the impacts on public health and the environment.

California has long been an oil-producing state, but it’s getting renewed attention because of the Monterey Shale, the country’s largest shale oil resource. It stretches under a large part of Central California. In places like Southern Monterey County, where new oil leases are being offered, the battle for fracking is heating up.

Vineyards and Oil Pumpjacks

Vineyards and farms stretch for 40 miles along the narrow valley around Highway 101, about two hours south of San Jose. “As a coastal growing region, we are the largest planted acreage of Chardonnay, so much more than Napa or Sonoma has,” says Kurt Gollnick of Scheid Vineyards, a winery in the foothills of Salinas Valley.

What Monterey County wineries lack is the name recognition that Napa has – and the visitors that follow. “This is something that we’re trying to change now. We do have very scenic areas of Monterey County,” Gollnick says.

Lately, the focus has shifted to what’s under the ground: oil – and plenty of it. On December 12th, the federal Bureau of Land Management is opening 18,000 acres for oil leases in Monterey, Fresno and San Benito Counties. Some parcels aren’t far from Scheid Vineyards.

Copyright ©, Pittsburgh Post-Gazette, 2012, all rights reserved. Reprinted with permission.

“This is where that whole conversation of fracking comes up,” Gollnick says. The oil deep in the Monterey Shale is notoriously tough to extract. Most if it is locked inside the shale rock. But recently, oil companies have gotten a lot better at getting oil out of shale thanks to hydraulic fracturing.

Millions of gallons of water, mixed with sand and chemicals, are injected underground at high pressure. That cracks the rocks, letting the oil out. Around the country, hydraulic fracturing has led to record levels of oil and gas production.

Shale Gold Rush

“Right now there’s a bit of a Gold Rush mentality concerning shale oil,” says Don Gautier, a geologist with the U.S. Geological Survey. He says fracking is nothing new in California. It’s been used for decades.

“What is new right now is that the price of oil is reasonably high. This technology has become very sophisticated. So these explorationists are justifiably optimistic about the idea of being able to get out oil that couldn’t have been accessed just a few decades ago,” Gautier says.

California’s oil shale resource is huge – more than 15 billion barrels in the Monterey formation, according to one estimate. It’s bigger than North Dakota’s oil reserve, where recently, thousands of wells have been drilled.

That has a lot of people wondering – is California next?

Debate Over Fracking

“There is absolutely a danger of California being transformed almost overnight as other areas of the country have been when the fracking boom hits,” says Kassie Siegel, a lawyer with the non-profit Center for Biological Diversity.

“In other parts of the country, we’ve seen contaminated water,” she says. “We’ve seen people who live near oil and gas wells complaining of health effects.”

Whether those impacts are specifically caused by fracking is under debate in many places, but Siegel says it’s enough to be concerned. Her group is suing the Bureau of Land Management over the oil lease sales, saying the agency has failed to review the risks that new fracking techniques pose.

Tight oil, or oil from shale, will be an increasingly large part of domestic U.S. oil production. North Dakota and Texas have more established oil shale operations than California. (Source: U.S. Energy Information Administration)

“They are acting as if nothing has changed in the oil and gas industry, but of course everything has changed,” Siegel says.

At the Bureau of Land Management office in Hollister, manager Rick Cooper says they’re offering the oil lease sale because of interest from oil companies. “Any time there’s new technology, then there’s going to be maybe a little buzz and a little interest in areas that hadn’t previously been developed,” he says.

The agency is predicting minor environmental impacts, however, because their analysis doesn’t forecast much new drilling.

“We haven’t seen development signals as of yet. But if we begin to see increased development, it would be at that time that we would pull back and say, well, we probably are going to have to do more analysis,” he says.

A Potential Shale Play

Several oil companies, including Venoco and Occidental, have reported they are experimenting in California’s shale formations. “Certainly our members are exploring how effective hydraulic fracturing is going to be in California,” says Tupper Hull of the Western States Petroleum Association, an industry group representing oil and gas companies.

Hull says California’s geology could be challenging for large-scale fracking. The shale layers are messy, bent by seismic forces. But he believes fracking has the potential to boost the state’s oil production, which has been declining for two decades.

“If hydraulic fracturing proves to be successful here as it’s been elsewhere, it’s an extraordinarily optimistic future we’re looking at from an energy point of view,” Hull says.

Back in Salinas Valley, Kurt Gollick says residents are watching. “I can tell you this from our perspective, farming is our number one source of income in Monterey County. It’s an eight billion-dollar industry.”

Gollnick says he hopes the two industries can coexist, but “if fracking introduces contamination to the water or anything else that affects growing practices, then that would be a huge point of conflict, no question about it.”

Bishop Ranch, San Ramon Fast Charger

Imagine pulling up to a gas station and finding out that the pumps aren’t working or that you have to be a subscriber to fill up.  Those are just a couple of the challenges that drivers of electric cars face as public charging stations slowly roll out. Alison van Diggelen, herself an early adopter, explores the growing pains of building an electric car charging network and the fledgling new industry rising up to meet the challenge.

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Range Anxiety – A Short Leash

Alison van Diggelen gets a fast charge with Ecotality's Blink network, Intuit Campus, Menlo Park

Electric vehicles are a popular and growing trend in California. But it can take hours to charge them, and there are only a handful of fast chargers in the whole state. I recently visited one of California’s  fast chargers at a Silicon Valley software company’s parking lot in Menlo Park, eager to get a charge for my all-electric Nissan Leaf. I’d traveled over 35 miles (that’s 70 round trip) from my home charger, and range anxiety had kicked in.

Eventually, I did make it home, but only after bypassing another fast charger that required I swipe a membership card which I don’t have.  I used an app on my phone to find the charger.

John O'Dell, Senior Editor at Edmunds.com says for electric cars to catch on it's vital to have a reliable charging network.

“Public charging infrastructure is critical to the widespread acceptance of plug-in and particularly battery electric vehicles. Because without public chargers you basically have a fairly short leash on your vehicle and you are not going to be willing to drive it long distances.” 

Although most driving and charging takes place within 40 miles of home, the lack of freedom to go much further has become a roadblock to purchasing electric cars for many Americans.

Loosening the Leash

Terry O’Day, with New Jersey-based energy company NRG, is hoping to loosen the leash on electric cars.    I caught up with him at a charger at a San Francisco parking garage. As part of a settlement over claims stemming from California’s energy crisis, NRG will install 200 fast-chargers and wiring for 10,000 standard chargers statewide by 2016.   NRG is calling its fast chargers, “Freedom stations.”

“You’re not tethered to a radius…this is much more like a gasoline fueling infrastructure where you can fast fill anywhere you need to go,” says O’Day.

Terry O'Day heads NRG's California charger roll out

Fast chargers can give fifty miles of driving range in fifteen minutes.  But because there are only a few, drivers usually opt for a standard charger, which can take more than three hours to get the same driving range.

Fast Charger Challenges

“We are looking for a well distributed network, like a cell phone network. It’s a small “d” democratic network that provides freedom to move within a region,” says O’Day.

Still, a multitude of challenges face NRG and other charging companies, like Bay Area-based ChargePoint and Ecotality. Fast chargers produce very high voltage. They require complicated permitting. And they cost upward of $40,000 each.

Right now, the financials don’t add up says NRG’s Terry O’Day.

“The public charging infrastructure is extraordinarily expensive and there aren’t enough cars right now so there isn’t an effective business model to make the investment work,” he says.

So how many companies does it take to install a comprehensive network of electric vehicle chargers?

“It’s not as simple as changing a light bulb,” says Ravi Brar, CEO of Ecotality, in San Francisco.  “It takes some effort, cooperation and coordination. It’s a sea change… a revolution in transportation. The biggest challenge might be that there are a hundred little challenges.”

But to date, there hasn’t been much coordination.   There are two different standards for fast chargers: one US-European, one Japanese. It’s much like the format war between VHS and Betamax. One of them will likely lose.

Japanese CHAdeMO fast charger and standard port on a Nissan Leaf

And to complicate matters, Tesla Motors, a leading electric car company, is building a proprietary network of fast chargers, which won’t work with either standard.

Pat Romano, CEO of ChargePoint in Silicon Valley, describes the current state of electric car charging as “somewhat of a mess,” but he’s optimistic the fast charger standards will get sorted out in time.

The Second Inning

Romano takes a long view and uses a baseball analogy, describing 2009 as the “first inning,” when modern chargers were first going in and electric cars were just being announced by car makers. Today, he says we are solidly in the second inning.

To date, about 50,000 plug-in cars have been sold in the U.S.  About one third of those sales were made in California, thanks to pioneering state rules that include rebates and carpool privileges for drivers of electric cars.

There are over 1000 public chargers in California today.  Romano predicts a tipping point by the end of 2014, when he expects to see hundreds of thousands of electric cars on the road and lots more chargers.

“When we hit about the 5th or 6th inning the mass market is really taking it up,” says Romano.

For early adopters like Terry O’Day, of NRG, it’s not surprising the demand is growing for electric vehicles.

“It’s quick off the line, unexpectedly fast, it’s quiet. You feel like you’re part of a revolution when you’re in the seat of an EV,” he says.

Like many enthusiasts, he believes more chargers will help boost electric car sales. Under the NRG mandate, fast chargers alone are set to quadruple in California in the next year. And just as all eyes were on California as the state launched its Cap-and-Trade program, the world will be watching to see if this public charger roll out helps jump start electric car sales in 2013.

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More resources on Electric Driving and Charging

Clean Car Diaries – over 25 stories from the Quest team on driving electric cars

Alternative Fuels Data Center – Dept. of Energy Resource for EV Charging, locations and incentives

Driving Electric – Online community for plug-in drivers

San Francisco BayLEAFs – Facebook community for Nissan Leaf drivers

Map of Charger Locations - Locations and reviews of all charger types, public and private, nationwide

Uncontaminated cells from a a salivary gland tumor. (Photo courtesy Osamu Tetsu)

Originally published July 13, 2012

Imagine you're a scientist, trying to cure brain cancer.

One thing you’d probably want to be sure of is that the samples you’re working with actually came from a brain tumor, and not some other kind of cancer.

This sounds like a simple problem to solve, but it’s been nagging scientists for years, causing the waste of precious research dollars.

Osamu Tetsu and Janyaporn Phuchareon learned that lesson the hard way.

Tetsu and Phuchareon are scientists at the University of California San Francisco’s Department of Head and Neck Surgery. They work in a lab, studying an obscure cancer of the salivary gland called salivary adenoid cystic carcinoma.

"Bingo!" (Or not.)

Researchers working on more common cancers may have dozens of cell lines to work with. But since salivary adenoid cystic carcinoma is relatively rare, Tetsu and Phuchareon had only six cell lines to experiment on, each of which could, theoretically, be traced back to a different patient.

One day, they noticed something that surprised them: Almost all the cell samples they were working with contained a virus. It was HPV virus, which you may have heard of because it can cause cervical cancer. To Tetsu, this looked like a breakthrough.

“I thought maybe the HPV infection is the cause of this disease,” he says.

In other words, they thought, maybe the HPV virus doesn’t only, potentially, cause cervical cancer, maybe it can cause salivary gland cancer too.

“We were very excited, says Phuchareon. We thought “Bingo! We might have something!”

Then they took a closer look.

They sent the cell line samples in for DNA testing. When the results came in, they learned those cells they’d been working with had nothing to do with a salivary tumor. Four of them came from a cervical tumor.

The famously vigorous HeLa cell is such a common contaminant of other cell lines that many laboratories refuse to work with it. (Image courtesy of ATCC)

These were HeLa cells, descendants of the infamously vigorous cervical cancer cell line that was the subject of the 2010 bestseller The Immortal Life of Henrietta Lacks.

The news was no better for the other two cell lines.

One of them, says Tetsu, didn’t show any DNA fingerprint at all. “That means this cell line is not human,” he says. They suspect both cell lines had become contaminated with mice cells somewhere along the line.

A silver lining

Six months of work, down the drain. But Phuchareon looks on the bright side. “It was bittersweet,” she says.

At least they found out before any major work had been done. They published a paper on their findings in a scientific journal, and have been able to warn other scientists who work on the same cancer.

“We think it’s important to have scientists know that this is a problem,” Phuchareon says.

The problem stems from the fact that, under a microscope, many cancer cells look the same. And since cell lines used in cancer research are anonymous, often shared informally between labs, the only way to definitively know where they came from is with DNA analysis.

The analysis is inexpensive, about $50 a sample. It’s the same technique used in crime labs. But not every scientist does it.

The steep price to science

In one 2010 case, three cell lines being used to research esophageal cancer all turned out to come from other cancers. Scientists had been working with these cells for years. They'd gotten major federal grants to do it, published more than 100 papers, even run clinical trials.

Some cell banks have estimated that as many as a third of their cell lines have been misidentified. These cell lines have been sent to labs around the world, for basic research.

Often, the results still hold. Misidentification is not a death knell for all experiments. But in many cases, cell misidentification can undermine research and waste millions of dollars, says Roland Nardone, a professor emeritus of biology at Catholic University in Washington DC.

“Money has been diverted away from useful experiments to meaningless experiments,” says Nardone.

A legacy of whistleblowers

Particularly frustrating to him is the fact that scientists have known about this problem for more than half a century.

One of the earliest scientists to call attention to it was a Bay Area researcher named Walter Nelson-Rees.

“He was a cultured man, as well as a very good biologist,” recalls Nardone.

Nelson-Rees was co-director of the Oakland-based Cell Culture Laboratory of the School of Public Health, funded by the National Cancer Institute.

In the early 1960s, he began running tests on commonly used cancer cell lines, to see how many were contaminated.

Gertrude Buehring — today, a professor of virology at UC Berkeley’s School of Public Health — worked down the hall from Nelson-Rees. She says every day, there was news of more contaminated cell lines.

“It was just one after another,” she recalls.

Many of the cell samples had been contaminated by HeLa. But not all.

“Some were interspecies contaminated, so that a human cell line actually turned out to be a mouse cell line,” she says. [Some lines that were supposedly] derived from a female turned out to be derived from a male.”

A career-ending discovery

Nelson Rees's discovery — that hundreds of cell lines had been misidentified — did not win him any friends.

Colleagues, says Buehring, “didn’t want to believe him. They fought him verbally at conferences. He was called a self-appointed vigilante and a lot of other names. One person even volunteered to send him a one way ticket to distant corners of the earth.”

Nardone says, at least initially, Nelson-Rees relished the fight.

“He was pugnacious,” says Nardone. “He recognized that he was going to be in a battlefield and he was ready for the fight.”

But, over time, the abuse took its toll.

“He seemed visibly upset that people couldn’t appreciate the service that he was doing,” says Buehring. “They were more worried about their own reputation.”

Nelson-Rees’s findings may ultimately have cost him his career.

“Without any explanation,” says Nardone, “his funds for support of his laboratory got smaller and smaller and he saw the handwriting on the wall and decided that was enough.”

Nelson-Rees became an art dealer. He died in 2009.

The search for regulation

A few years ago, Nardone decided to devote his retirement to the problem that Nelson-Rees had publicized. He joined a workgroup, led by the Virginia-based research nonprofit ATCC, to come up with a standard, one that all researchers could work by.

The standards, which came out this year, outline the correct way to authenticate cell lines, so that researchers can compare results from lab to lab. ATCC also maintains a list of misidentified cell lines on its website.

The ATCC’s Liz Kerrigan says the challenge has been getting scientific institutions to adopt the standard.

“Surprisingly to most members of the workgroup, there has been resistance to addressing or even acknowledging the problem,” she says.

A few influential science journals now require that scientists authenticate cells before they’ll publish their results. But Nardone and Kerrigan believe that’s too late.

Much better, says Nardone, would be to get the big funding institutions, particularly the National Institutes of Health, to demand that anyone who applies for funding for cell-culture research authenticate their cell lines initially.

In other words, get the cells checked out before the money’s spent.

The NIH steps back

In a statement, the NIH said doing this would be, quote, “impractical,” and that it trusts researchers to do the right thing.

Kerrigan and Nardone believe that the costs of misidentified cell lines call for greater oversight.

“The consequences of widespread misidentification of cell lines is immeasurable, really,” says Kerrigan. “In addition to the waste of millions of dollars, there’s time, intellectual resources. And then people lose confidence in published work.”

They’re hopeful stronger policies will soon emerge.

On August 6th, a fire broke out at the Chevron oil refinery in Richmond, hobbling refinery operations, contributing to a statewide spike in gas prices, and sending 15 thousand people to nearby hospitals, complaining of headaches, dizziness and other ailments.

For a lot of residents in Richmond, it was the last straw in a long, rocky history with the Chevron refinery.

At a recent meeting of the Atchison Village Neighborhood Council, just over the fence from the refinery, residents John Gordon and John Kendrick, were still complaining about Chevron’s community response in the wake of the fire.

“They came out in the newspaper said there were no explosions,” says Kendrick. “I heard four!”

“Boy, are they sleazy!” Gordon exclaims, as long-time community activist Andres Soto chimes in. “We live here. We know they’re going to lie to us.”

Even among those less cynical of Chevron’s intentions, the fire re-ignited questions many have been asking for years: What does it mean to live next to the largest refinery on the West Coast? What are people here breathing?

They are difficult questions to answer in a city thick with industry and transportation.

A storage tank at Chevron's Richmond refinery.

“It’s probably not all Chevron,” says Kendrick. “We’ve got the railroad cars, we got the highways, we got trucks coming going. But it’d be nice to get a breakdown to understand.”

Monitoring the air

Despite a century of industry in this area, there are only two official air-quality monitors in Richmond, and two in nearby San Pablo. They’re both run by the Bay Area Air Quality Management District. The August fire revealed a system designed to look for averages over time not illuminate emissions from specific incidents or indicate where they come from.

To Larson, an air-monitoring activist who heads the non-profit Global Community Monitor, that’s just not enough.

Air monitoring advocate Denny Larson heads Global Community Monitoring, a nonprofit.

“We have a high concentration, probably hundreds of toxic emissions sources in a very small area. And the wind is almost always blowing from where those industries are to where people are breathing in north Richmond,” he says.

Pretty soon, residents will know at least a little more about what it is, exactly, they’re breathing thanks to a new network of monitors being put in by the very company many of them so deeply distrust: Chevron.

Industry fills the air-monitoring void

The six new monitors are designed to pick up common industrial chemicals including benzene and sulfur dioxide. One of them will be on, or near, the Shields-Reed Community center in North Richmond.

Says Larson, “we’re going to take a quantum leap into the 21st century when the Richmond system is in because we will then be able to better identify what the sources are.”

One of Richmond's new air monitors will be at this North Richmond community center.

Chevron agreed to pay for this new system – including about a million dollars of equipment in addition to an online, publicly-accessible reporting system — as part of a settlement with the city back in 2010, but the project stalled. After the August fire, the pace picked up.

The plan, says Chevron spokeswoman Heather Kulp, is to have a third-party contractor, independent from Chevron, providing real-time results and quarterly reports to the public.

“We are not filtering,” says Kulp. “We have nothing to do with the data. So the community can have a lot of confidence in this data because it’s going directly from the instruments to the web.”

Larson says he endorses this system, but the community will have to stay vigilant.

“Even after it’s up, we have to make sure that they don’t make any changes to the system or forget to pay the contractor, whatever. If we’re not watchful, the system won’t be successful in delivering information people want.”

But among those in Richmond whose job it is to keep the air clean, this whole plan is raising some eyebrows.

Will the data have teeth?

“I was surprised to see the agreement [between Chevron and the city of Richmond]”, says John Gioia, Contra Costa County Supervisor and chair of the Bay Area Air Quality Management District.

Gioia says because the monitors are being operated outside of government oversight, the results aren’t certified. Even if the monitors showed something toxic being released into the air, there’s not much officials could do about it, other than follow up with their own testing.

“The air district can't use that data to impose a fine or penalty,” he says.

Complicating things is the fact that the Air District is also stepping up its own monitoring in the wake of the fire. Plans are afoot for a new monitoring network around all five of the Bay Area’s refineries, including Chevron.

These plans are just getting started, but the idea is to make refineries pay for the cost of installing and operating that system, through fees that the District has the authority to levy.\

"Information is power."

Denny Larson, the activist, says he’s not worried about a conflict here — the more monitors, the better. Information, he says, is power.

Larson already knows what one of the first questions will be. It has to do with a giant wastewater treatment pond that Chevron uses to filter out toxic chemicals.

Refineries in Europe often cover these ponds, to collect fumes that would otherwise drift into the neighborhood. But here, the ponds are uncovered. Larson would like to see that changed, but that’s hard to do without accurate data about what emissions the ponds produce.

“We can’t get very far without saying look, that’s a big source of toxic pollution. We want it covered and we don’t want those vapors coming into the neighborhood anymore.”

Will the air monitors give residents ammunition to make Chevron change its ways?

Chevron doesn’t think so. In fact, refinery spokeswoman Heather Kulp thinks the monitors will have the opposite effect.

“I think what they’re going to see is to understand that there are multiple sources of emissions in this community. And I also think they’re going to see that the air quality in Richmond is actually a lot better than they believe it to be.

Chevron says its six new air monitors – that’s three on the refinery, three in nearby neighborhoods — will be up and running in a few months. The other system – those government-run monitors that could actually help set fines – could take several years.

(Photo by Justin Sullivan/Getty Images)

This week, California rolls out the heavy artillery in its attack on climate change with a program called “cap-and-trade.” It’s like a stock exchange for carbon emissions, where the state’s biggest polluters have to buy the right to emit greenhouse gases. It’s the most ambitious climate change policy in the country, but not everyone is happy with it.

So how does it work?

(Check out the radio story above for an explanation involving poker chips, musical chairs and Monopoly money.)

The first part is the cap. Until now, businesses haven’t had to worry about how much carbon they emit from burning fossil fuels. Now, there’s going to be a cap on total emissions. At first, they can emit about as much carbon as they have been. But then, the cap on emissions begins to come down.

More than 300 businesses, from power companies and oil refiners, to glass makers and food processors, are required to participate in the cap-and-trade program. The government could tell each company how much it’s allowed to pollute, or set a tax on carbon. But California’s doing it differently by creating a market. That’s where the “trade” part of cap and trade comes in.

In order to keep up with the lowering emissions cap, businesses have three choices. The first is pretty straightforward: reduce emissions.

The second option is to buy permits to pollute. The state will give companies allowances — each allowance grants a company permission to emit one ton of carbon dioxide. Companies can buy and sell allowances on the carbon market.

And the third option is known as "carbon offsets." Companies can essentially pay other organizations to reduce greenhouse gases, for instance, by protecting forests. Each offset counts toward the firm's compliance obligation, though companies are limited in how many offsets they can use.

But will it work?

California has been preparing for this moment for a long time. When Governor Arnold Schwarzenegger signed AB 32, the state’s landmark global warming bill in 2006, he set an ambitious goal: to cut California’s greenhouse gas emissions 30 percent by 2020. Cap-and-trade is supposed to help accomplish a big part of that goal.

"We want to reduce the amount of pollution, but we want to do it in a way that isn’t too costly to the economy," says UC Berkeley economist and energy analyst Severin Borenstein at UC Berkeley. He says the market will create some flexibility for businesses.

But some businesses aren't so sure about it.

"I am very very worried about this program," says Dorothy Rothrock from the California Manufacturers and Technology Association, which represents about 700 companies. Her members are concerned that cap-and-trade will put them at a disadvantage to companies outside of the state.

And Rothrock says the costs will eventually be passed on to consumers. For instance, the price of gas may go up. "It’s not like they’re suddenly gonna see a big bill in their mailbox the next day, but the costs will be coming and there won’t be a lot we can do to stop it," she says.

California has taken steps to minimize this impact. At first, nearly all of the allowances are free for businesses, and some of the proceeds from the carbon market will go to communities hardest hit by pollution. Regulators also argue that the gains in energy efficiency spurred by the program will outweigh any higher costs.

And environmental advocates point out, if we don’t cut emissions now, the impacts of climate change will be even more expensive in the long run.

Emily Reyna with the Environmental Defense Fund says it’s important for California to take the lead.

"If it’s done right here in California, which I believe it will be, then it can be a real model for the rest of the country, the rest of the world," she says.

On Wednesday, all eyes will be on California, when the state's carbon market opens for the first time.

A worker handles solar panels at SunPower's manufacturing plant near San Jose.

Talk to anyone in the solar industry and they’ll tell you: it’s the best of times, it’s the worst of times. Solar installations are booming, but there’s also a looming trade war with China. Citing illegal subsidies, U.S. officials have placed trade tariffs on Chinese solar panels. American solar companies are split on whether it will be good or bad for the industry.

A Solar Manufacturer

At SunPower’s solar manufacturing plant near San Jose, workers screw frames onto shiny, six-foot solar panels as they come off the line. “We are running 24 hours a day,” says quality engineer Eric Kao.

This plant has had a long list of notable visitors: Governors Jerry Brown and Arnold Schwarzenegger, Energy Secretary Steven Chu. That’s because SunPower is one of the top suppliers in the country — and because there aren’t many solar plants left to visit. It’s getting lonely to be an American solar manufacturer.

“It’s going to require being lonely to be one of the winners but it’s unfortunate that there aren’t many American solar companies,” says Tom Werner, CEO of SunPower. He says five years ago, things were looking good for U.S. solar manufacturers. There were growing markets in Germany, Japan and California.

“Many of the industry participants were making good profits. Well, that attracts competition,” he says. Chinese manufacturers flooded the market with solar panels. Within four years, panel prices fell seventy five percent.

“The economics have gotten way, way more challenging. It's difficult for some companies to make it,” Werner says. SunPower has survived, but is just hoping to break even this year.

Last year, several American solar panel companies filed a trade complaint against China, saying Chinese solar companies are getting illegal subsidies and are dumping panels on the US market. In May, the U.S. Commerce Department agreed and levied trade tariffs of 25 to 35 percent.

Werner says while SunPower didn’t directly join the complaint, it does stand to gain. “Let’s just say it won’t hurt our pricing but I don’t know if it will be a big advantage. Having a trade war is definitely not good for the industry so we need to sort this out.”

The solar industry doesn’t need more bad news, says Werner, especially after the political scandal over one particular bankrupt solar company. “It’s amazing how many people know the name of that company.”

Solyndra, that is. It’s a name Werner avoids saying, much like like Lord Voldemort in Harry Potter. “Well see, if I name the company then I’m just propagating the whole deal,” Werner says. Tariffs or no tariffs, Werner says some US manufacturers may not make it either. It’s an entirely different story with solar installers.

Flip Side: A Solar Installer

At Sungevity’s Oakland headquarters, a team of sales people grabs maracas off their desks. “So the maraca shake happens when there’s a sale,” says Danny Kennedy, president of Sungevity.

Sungevity is one part power company, one part internet startup. It designs residential solar systems virtually by using satellite photos of each house. Like online shopping, Sungevity makes a sale before a truck ever goes out. And sales have been good.

“We grew gangbusters in 2010. Doubled again in ‘11. Have continued to grow this year,” says Kennedy. That’s thanks to a new option for customers to lease a solar system, instead of buying it upfront. It’s also more affordable because panels are cheaper.

“This is something I think we should celebrate – the fact that we’re driving cost out of clean energy,” he says.

Sungevity buys panels from the US, Korea and from China. Even with the trade tariffs, prices are about the same because Chinese solar companies have found a loophole. The tariffs are only on solar cells, not the entire solar panel. So, the cells are manufactured offshore and put into panels in China.

But Kennedy says focusing on these manufacturing jobs is a mistake. The real green jobs are elsewhere. “There’s more job density in the sales, finance, installation and maintenance end of the value chain than there is in the factory. It’s probably a ratio of three to one.”

California leads the nation in solar jobs. Kennedy is concerned that a trade war with China would put them at risk.

“It’s crazy talk. We’re growing faster than any industry over a hundred billion dollars in value in the global economy. And yet, there is this nabobs of negativity around us that are causing concerns in the investment community,” says Kennedy.

Solar’s Teenage Years

All of this adds up to some major growing pains for the industry. “It is totally a teenager in a lot of ways,” says Dan Kammen, a professor at UC Berkeley.

“The industry is growing dramatically. There’s also incredible turmoil. And there are some teenagers who are clearly going to be young prodigies and others who are going to go into rehab,” says Kammen.

When companies fight over market share and race to the lowest price, Kammen says it’s the startups with cutting-edge technology that just can’t compete.

“A battle between the two biggest players, the US and China, is one where we might actually have casualties that aren’t just business casualties, they’re actually, pieces of innovation getting lost.”

The trade tariffs won’t be final until the US International Trade Commission rules on whether China has been illegally subsidizing their solar industry. That decision is expected on Wednesday.

NIF's 192 lasers culminate inside this target chamber, which contains the hohlraum. Credit: NIF

The National Ignition Facility in Livermore, California, has been called a modern-day moon-shot, a project of "revolutionary science," and "the mother of all boondoggles."

NIF, as it's known, is a five-billion dollar, taxpayer-funded super laser project whose goal is to create nuclear fusion – a tiny star – inside a laboratory. But so far, that hasn't happened.

The facility, which began operating in 2009 after a decade of construction at a cost of almost $4 billion, points 192 football-field-sized lasers at one tiny capsule the size of a peppercorn and filled with hydrogen. It creates degrees of heat and pressure never before achieved in a lab.

Standing outside NIF’s target chamber in 2008, about a year before NIF’s dedication, Director Ed Moses called NIF “more far-out, and far cooler than anything in science fiction or fantasy.”

A tiny star for a blip in time

“For a brief period of time, not a hundredth or a thousandth, but a billionth of a second,” explained Moses, “we will raise the temperature of the target to a hundred million degrees.

“That’s higher temperature and more pressure than exists at the center of our sun. It’s a hundred million times more pressure than you’ll find at the deepest part of the ocean.”

Under those conditions, the hydrogen atoms could enter into a state of controlled nuclear fusion. (In nuclear fission, as in nuclear power plants, energy is generated by splitting atoms. Fusion is the opposite: Atoms are smashed together.)

The goal is referred to as “ignition.” It would put out more energy than the lasers had put in to it.

192 powerful lasers create star-like conditions inside a peppercorn-sized "hohlarum." Credit: NIF

If scientists can make ignition happen at NIF, that achievement could, theoretically, be parlayed into a new kind of nuclear power plant. Unlike fission plants, which eat up uranium and generate radioactive waste, these fusion plants would run on water, and create virtually no waste at all.

Waiting to ignite

At NIF's dedication in 2009, George Miller, then-head of the Lawrence Livermore National Laboratory, seemed to believe that ignition was right around the corner.

“I think we will get ignition,” Miller told the crowd. “I think we'll get ignition relatively shortly after we turn the facility on.”

Since then, the strength and functionality of the lasers have received praise from the physics community.

“The laser has been working phenomenally,” said Christopher Deeney, who directs the Division of Defense Science at the National Nuclear Security Administration, which oversees NIF. “It's the most controllable, precise laser the community has ever built.”

But ignition – the goal at the center of NIF’s name — hasn’t happened. “We just haven't gotten it to burn yet,” explained Moses at a recent interview.

Inside NIF, a football-field sized array of lasers. Credit: NIF

In a July 19, 2012 report, the NNSA concluded that “the probability of ignition before the end of December is extremely low.” The report called the functionality of the lasers “outstanding,” but blamed NIF’s computer simulations for the failure to ignite.

An NNSA ignition deadline of October 1, 2012, has now come and gone.

Moses bridles at the idea that anyone can put a deadline on this achievement.

“We never guaranteed anything on any particular date,” he says. “People have to sort of get used to that. That’s what great science is.”

Nevertheless, by law, on November 30th, Department of Energy Secretary Steven Chu is required to report to Congress on why NIF hasn't met its goal, despite significant cost to taxpayers: about 300 million dollars a year on top of over three billion in construction costs.

For Christopher Paine, a longtime NIF critic with the Natural Resources Defense council, this amounts to an “I told you so” moment.

“This project has gone on a long time,” he says, “billions of dollars invested. But to what end?"

What is NIF for?

Paine's criticism of NIF boils down to two objections: the project's expense and what you might call a muddled sense of purpose. What, in other words, is NIF for?

There are three answers to that question, explains a 2009 NIF promotional video.

“NIF will explore controlled nuclear fusion to ensure global security, enable sustainable clean energy, and advance our understanding of the universe.”

Let’s break that down.

Reason number one: Global security. This is the primary intent of NIF, and it has to do with the fact that actual nuclear bomb tests have been banned worldwide.

Because NIF simulates a nuclear reaction in a tiny pellet, you could test the strength of nuclear bombs without having to actually explode them.

Paine believes that’s unnecessary. "We haven’t had NIF for the last 20 years," he says, "and we've been maintaining the stockpile."

NNSA"s Deeney disagrees, calling NIF a “key element in our stockpile stewardship program.” He says important experiments can be done at NIF even without ignition. “We're committed to NIF for the long term,” he says.

Reason number two: Clean, fusion energy. This is a very long-term goal. Even if NIF does achieve ignition, it could take decades to adapt that technology into a working fusion power plant, something that could power a light bulb in your house.

A 100-year solution to a 20-year emergency

Paine says with climate change, we don't have that kind of time.

“Dealing with climate change is a 20-30 year planetary emergency,” says Paine. “Fusion energy is irrelevant to that timescale. Humanity needs to change its ways now. It needed to change its ways yesterday. Fusion energy is a 50 to 100-year project with no assurance of success.”

At NIF, the goal is to create nuclear fusion — a tiny star — inside this peppercorn sized "hohlraum." Credit: NIF

But it's the third reason, to “advance our understanding of the universe,” that Moses emphasizes these days.

“The Higgs Boson was just discovered at the [Large Hadron Collider] in CERN, at a cost of ten billion dollars,” he points out. “Was it late? Was it early? Was it on time?”

The answer, he says: Who cares? Moses calls these types of projects “grand challenge science,” and insists they cannot be performed on deadline.

“It’s not grand challenge science if you know the answer before you start,” says Moses. “And this is exactly that.”

NNSA's Christopher Deeney also declines to predict when NIF will achieve its goal.

“Right now we will not make a prediction of when ignition will happen,” he says. “It's still a discovery science project. Right now it's unpredictable.”

That's the case NIF's advocates will have to make to Congress at the end of this year. It’s worked so far. After all, NIF has something for both sides of the aisle: Democrats like clean energy, Republicans like weapons security.

But everyone likes a breakthrough, and at NIF, that's still out of reach.

A sustainable city built from scratch: That's what developers are aiming for with Tianjin Eco-city. Photo: Marjorie Sun

From green building rules to carpool privileges for electric cars, California has moved in recent years to plan for a more sustainable future. It’s a trend here, but nowhere is the urgency greater than in China, where hundreds of millions of people are moving to cities in pursuit of a better life.

China’s urbanization has come at a tremendous cost: pollution, traffic congestion, surging energy use and more carbon dioxide emissions. Now, China is partnering with experts in the Bay Area on a huge experiment—building new cities to be environmentally sustainable.

China’s Eco-city Showcase

Zhang Xi is a pretty, willowy woman. And she’s an urban pioneer. She and her family are among the first tenants of Tianjin Eco-city, a showcase for China’s push to build sustainable cities from scratch. Zhang moved here from Beijing, about an hour to the north by bullet train. She was enticed by a new job and a shorter commute to work. Much shorter.

“It’s just three minutes by elevator, so it's really convenient,” Zhang told me through a translator. She "used to take the subway for half an hour, then change to a bus. That would take one hour."

Now Zhang, a customer service rep, lives and works in the same high-rise. Her quick commute—albeit an extreme case–is one of the core principles of an eco-city: cut car use. Walkable streets are key too– short city blocks, intersections that are easy to cross.

The area bears no resemblance to what was here just a few years ago. "When this project was first conceived in 2007, this was just a barren site,” said Ho Tong Yen, CEO of the company developing the Tianjin Eco-city and the visionary for this $8 billion experiment. “It comprised saline and alkaline land, polluted water bodies. There was nothing inherently ‘eco’ about this site at all."

But with the backing of the governments of China and Singapore, developers cleaned up the site. Clusters of new high-rises now dot the flat terrain here, with more under construction. There’s a mix of public housing and private, upscale apartments, all built to be energy-efficient.

Five thousand families have already bought homes here. By 2020, if plans pan out, Tianjin Eco-city will swell to 350,000–nearly the size of Oakland. This development is one of dozens of pilot projects around China spearheaded by the central government to serve as models for future cities.

Rural Migration Fuels Urban Problems

The need is urgent. In the past year, the number of people living in cities here surpassed the rural population for the first time. While this migration has fueled China’s remarkable economic boom, major cities–like Beijing—are beset with pollution and traffic congestion, which wastes energy. What’s more, commutes between home and work are often long, which means more pollution and greenhouse gases. That’s because single-use zoning often separates commercial districts from residential areas.

The problems are sure to worsen without better planning. By 2030, as many as 300 million more Chinese are expected to move from the countryside to urban areas. That’s enough people to create 79 cities the size of Los Angeles.

Tapping California for Advice

So to prepare for that, several Chinese cities have partnered with a Bay Area firm for advice. One tip they got from Peter Calthorpe, president of Calthorpe Associates, an urban design group based in Berkeley: good urban design comes first, then add clean technology.

When the mayor of a major Chinese city asked Calthorpe to redesign an area for a million-and-a-half people, the first things to go were the really long city blocks that are typical here. "We got in and modified the street system so there were more human-scale blocks and smaller streets everywhere,” says Calthorpe. “We mixed the land use so you didn’t have to walk very far to school, parks or stores. And we concentrated development around the transit stations.”

Calthorpe has applied some of the same principles to projects in the Bay Area, including new developments at Alameda Point and Bay Meadows in San Mateo.

How ‘Eco’ is Tianjin Eco-City?

But Tianjin Eco-city executive Ho Tong Yen says, "There is no one definition of what it means to be an eco-city. So what we have done is put together a set of key performance indicators, which we think are stretch targets; they are ambitious but achievable.” Those include 20% of the town’s electricity from renewable sources (low by some standards today), and half its water from harvesting rain and other “non-traditional” sources.

At a popular new Korean restaurant in Tianjin Eco-city, it’s lunchtime and the place is packed. The restaurant is just a couple minutes walk from apartments and offices. Eventually there will be a light rail system and a large park extending through the middle of the city. But clearly there are still some design flaws to work out.

"So just to get around the corner and up the street you have to walk a really long way,” says Cecilia Springer. She’s a Fulbright scholar who’s studied Tianjin Eco-city. “You can't really cut through the middle of the blocks." She also points out that to get to the closest major city center–in Tianjin–you have to get in a car and drive at least a half an hour. "So one could call it a Chinese suburb,” Springer says, “and that raises a lot of questions of how green can a suburb can really be."

Another valid question is how many “green suburbs” it will take to arrest the environmental consequences of China’s economic growth. It’s a race against time as millions more migrate to the nation’s cities and China’s growing middle class pursues a more comfortable, “Western” lifestyle.

This crisis has led the VA to explore treatments that would have been considered decidedly from-the-fringes a generation ago. Some of that work is taking place at the Menlo Park division of the VA Palo Alto Medical Center.

"My little safe zone"

John Montgomery is a Vietnam vet with a bushy gray mustache and a tattoo of a scorpion on each forearm. During his time here in the residential PTSD program, he’s been thinking a lot about his life before the war.

“We were dirt farmer kids,” he tells me. “It was the summer of 1957. We were irrigating 80 acres of cotton. My brother was yelling off in the distance and I was just laying back on a haystack…”

Montgomery trails off for a moment, lost in the memory.

“Yeah, that's my little safe zone,” he says.

But when he talks about Vietnam and what he saw there, something in his voice changes, ramps up.

The image he can’t shake – even now, nearly four decades after his return – is of Vietnamese children trying to kill him.

“Our society teaches us to go to school, live with our families and stuff, not to blow somebody else up," he says, as his voice grows louder. "They were after you, you know?”

Today, after what he calls decades of failed relationships and self-abuse, Montgomery is finally getting help for PTSD, a diagnosis he hadn’t even heard of until a few years ago.

Part of his treatment is a twice-weekly guided meditation session.

On a recent afternoon, five men settle into armchairs arranged in a circle. One younger vet in board shorts and flip flops lies down on the floor. Two of the vets served in Vietnam; three younger men served in Iraq. A couple of therapy dogs, golden retrievers named Eldridge and Elaine, settle at their owners’ feet.

Leah Weiss — a meditation trainer from Stanford’s Center for Compassion and Altruism Research and Education — begins to lead. “Let’s start with three deep cleansing breaths,” she tells the men.

An old approach, revisited

What’s taking place in this room has been happening on a small scale for decades, says Stephen Xenakis. He’s a retired brigadier general who formerly oversaw the army’s medical system.

In the 1970s, Xenakis worked as a psychiatrist with Vietnam vets at the former Letterman Army Medical Center, in San Francisco’s Presidio. He says meditation was one of several Eastern-inspired treatments he and others were experimenting with.

Even back then, he says, it was clear that meditation could help calm the nervous systems of not just veterans, but prisoners and people suffering from trauma.

But getting the VA to integrate meditation into its standard treatment was tough, especially after the late 1980s, when drugs like Prozac came on the scene. The drugs were easy to study and prescribe, cheap to administer. For a lot of patients, they were very effective.

“I think in many ways,” he says,” these other options that we had learned were helpful back in the ‘70s kind of fell off to the wayside”.

In recent years, it’s become clear that drugs are no panacea. Side effects are common. And for about half of PTSD patients, the drugs don’t work at all. A recent report from the Institute of Medicine concluded that "the evidence is inadequate" to demonstrate that SSRIs, like Prozac, are generally effective in treating PTSD.

Those limitations have renewed interest in other approaches, such as meditation.

What meditation may do to the brain

Back in the TV room at the Menlo Park VA, Weiss’s voice is calm, almost hypnotic. She tells the men to “bring to mind a stranger, maybe someone you pass by when you’re commuting.”

“Consider,” she instructs them, “that just like me, this person has had ups and downs in his or her life. Just like me, this person has had goals and dreams. Just like me, this person knows what it’s like to be disappointed, or afraid.”

This particular meditation -– it’s called “compassion meditation” — aims at a specific and widely held hypothesis about what is happening in the brain of someone like John Montgomery, the Vietnam vet.

The idea is that in combat, a switch — a fight-or-flight survival mode located in a part of the brain called the amygdala — has been turned on, and become essentially stuck. Meanwhile, another part, the frontal cortex, takes the backseat. And that’s critical. Because this part of the brain helps us relate to other people.

“The frontal cortex,” says Stephen Xenakis, “is what allows us to have relationships and families, what gives us a sense that there are rules of society and morality. It's part of what is different about our brains from even other primates, and clearly other mammals."

Whether or not this kind of meditation is effective in treating PTSD is, from a scientific standpoint, still unknown. Studies have shown that repeated sessions can increase "positive affect" and "social connectedness," both of which are deficient in PTSD patients, according to a 2012 meta-analysis on the efficacy of different kinds of meditation in treating PTSD.

Meditation in general, wrote the authors, "holds some promise" as a treatment for PTSD.

Advice from an older veteran

After about 20 minutes, Weiss asks the men to open their eyes and to reflect on what the meditation made them feel.

Most of these men have been taking part in these sessions for a couple months now. They’ve been listening to CDs with Weiss’s voice back in their rooms. They say they feel calmer, more compassionate to other people.

But one of them, Esteban Brojas, is newer to this. Brojas served during the Iraq invasion in 2003. In some ways, he says, it’s like he’s still there.

Coming back to civilian life has been “a culture shock,” he says. “You’re still with that adrenaline; you’re still hyper-vigilant.”

Brojas’s wife gave birth to their daughter while he was in Iraq. When he came back, he didn’t know how to hold her. “After taking someone's life? It’s hard,” he says.

As he speaks, Brojas’s voice starts to tremble and speed up. He rubs his hands together quickly as he rocks back and forth in his armchair.

“After the fact that you're going into a building and there's a grenade being popped and there's a woman and a child in there? It's hard. To come home and hold your daughter in your hands?”

Doreen, the therapist steps in. “I would say…” she begins, tentatively.

But it's John Montgomery, the Vietnam vet across the room, who knows what to do.

“You're not there,” he tells Brojas, firmly. “You're right here. You're not there right now. You’re in it. It'll take time. It's like a wave coming. It’ll subside.”

Montgomery’s doing something he thought he had forgotten how to do: feel compassion. In a few weeks, he’ll leave this program and go back to his family – a different man, he hopes, than he was when he came here.

Dr. Shinya Yamanaka, stem cell researcher at the Gladstone Institutes, in San Francisco, won the 2012 Nobel Prize in medicine. (Credit: Jenny Oh)

Reported for KQEDnews.org

Shinya Yamanaka, a stem cell researcher at the Gladstone Institutes, which is affiliated with the University of California, San Francisco, has won this year’s Nobel Prize in Physiology or Medicine jointly with English researcher John B. Gurdon.

Yamanaka, who is also an investigator at Kyoto University, in Japan, and a professor of anatomy at UCSF, won the prize for developing a technology to create stem cells that can become any type of cell in the body. His method creates cells that are like embryonic stem cells, without using human embryos.

These so-called induced pluripotent stem cells, or IPS cells, could one day lead to cures for a wide range of diseases, from Parkinson’s to heart disease. And they bypass the ethical issues surrounding the use of human embryos for research.

IPS cells are like embryonic stem cells in that they can be coaxed into becoming any type of cell in the body. But unlike embryonic stem cells, which are created from human embryos, IPS cells are developed by introducing a few genes into common adult cells like skin cells.

“We knew that embryonic stem cells and skin cells, although they are very different, have the same blueprint, which consists of approximately 30,000 genes,” Yamanaka told KQED News during an interview at the Gladstone Institutes in San Francisco in 2010. His method consisted in getting the skin cells to “read” the genes that give embryonic stem cells their qualities.

In announcing the award today in Stockholm, Sweden, the Nobel Committee for Physiology or Medicine said that "These groundbreaking discoveries have completely changed our view of the development and cellular specialization. We now understand that the mature cell does not have to be confined forever to its specialized state."

Yamanaka won the award jointly with John B. Gurdon, from the University of Cambridge and the Gurdon Institute, in Cambridge, England. The Nobel Committee recognized Gurdon for his pioneering work in animal cloning. In 1962, Gurdon discovered that "the specialization of cells into different tissues is reversible," said the Committee.

Yamanaka, who was an orthopedic surgeon before becoming a research scientist, became interested in stem cells as a way to potentially help patients suffering from spinal cord injuries, for which there are no treatments today. He decided to look for an alternative to embryonic stem cells in response to the controversy around the use of embryos for research.

“What I’m hoping is that by using IPS cells, which are free from ethical issues, we can speed everything up,” he said.

Though funding is available in California for researchers using embryonic stem cells, federal funds have been subject to the political pendulum. President George W. Bush restricted funding in 2001. On his first day in office in 2009, President Obama overturned Bush’s decision and made federal funding available for the research.

In 2006, Yamanaka was able to create IPS cells from mice adult cells. His big breakthrough came in 2007, when he created the embryonic-like cells from human skin cells. He then took these IPS cells, and using their ability to become any cell in the body, coaxed them into becoming heart cells. Proof of his success arrived in the form of an email from a researcher at his lab in Kyoto.

“I was in San Francisco. He sent me a video showing beating heart cells,” Yamanaka said. “But those heart cells were not from a heart. They were actually from skin.”

In this 2008 NOVA ScienceNow video, Yamanaka explains how he made his breakthrough.

Treatments based on IPS cells would be based on their ability to become stem cells that could regenerate damaged cells in different organs. Yamanaka said that stem cell transplants on animals with spinal injuries have shown promising results in his lab. Clinical trials could be five years away, he said. He is also using IPS cells to test drugs against Lou Gehrig’s disease.

In addition to bypassing the ethical issues, IPS cells have another advantage over embryonic stem cells. Because they’re created from patients’ own cells, they would be less likely to be rejected by their bodies.

Since Yamanaka’s breakthrough, scientists have taken his cellular reprogramming techniques one step further and are now able to transform one type of adult cell directly into another, bypassing the stem cell stage altogether. Deepak Srivastava and his team at the Gladstone Institute of Cardiovascular Disease have created beating heart muscle cells in mice from another type of heart cell that normally becomes scar tissue after a heart attack.

Yamanaka is only the second Japanese scientist to win the Nobel Prize in medicine. In 1987, Susumo Tonegawa, from the Massachusetts Institute of Technology, received the award. Yamanaka said he plans to use his award money to fund young researchers.

Yamanaka, 50, spends a few days each month in San Francisco working at the Gladstone Institutes, where he began his research career in 1993 as a postdoctoral fellow.

He lives in Osaka with his wife, a dermatologist, and two daughters, aged 22 and 20, both of whom are in medical school.

“I’m the least busy person in my house,” he joked.

Stem cell researcher Shinya Yamanaka talks about how he created embryonic-like stem cells from skin cells; when treatments might be available, and why researchers still need to study embryonic stem cells.

Watch:
QUEST's story explaining what stem cells are and how researchers hope to use them to develop treatments for heart disease.

When San Francisco voters head to the polls in a few weeks, they’ll be weighing in on one of California’s oldest environmental battles. A large part of San Francisco’s water supply is stored inside a national park – in a reservoir built in Yosemite’s Hetch Hetchy Valley.

Environmentalists all the way back to John Muir have called on the city to store its water elsewhere so the valley can be restored. A November ballot measure would require the city to develop a plan to do that. But the battle over Hetch Hetchy is just as fierce today as it was a century ago.

It’s evident when you drive up to the entrance booth in Yosemite National Park on your way to Hetch Hetchy Reservoir. The ranger hands you a brochure from the San Francisco Public Utilities Commission that reads: “20th century engineering marvel. Hetch Hetchy Reservoir is the keystone of this clean, efficient water and power delivery system.”

Why would a city agency pass out promotional pamphlets about a reservoir? Probably to respond to people like Mike Marshall.

“This belongs to the American people. And what we can do – what San Francisco can be leaders in is draining this and bringing this incredible place back to life,” says Marshall, director of Restore Hetch Hetchy.

His group has a singular goal: drain the reservoir and make the valley a second Yosemite Valley. And for the first time in decades, that goal is in reach. Measure F on the San Francisco ballot would require the public utilities commission to draw up a plan, at the cost of $8 million, for draining the reservoir and finding new water storage. In 2016, that plan would go before San Francisco voters.

Hetch Hetchy Valley in 1906. Photo: USGS.

“We thought ‘what a great debate to have.’ Now that we know what we know, should we revisit a decision 100 years ago that had huge environmental consequences?” Marshall says.

History of a Valley Turned Reservoir

Yosemite was already a national park when San Francisco went looking for a reliable water supply a century ago. The idea for a new reservoir didn’t get much traction until the 1906 earthquake, when much of the city burned to the ground. “They used that as a rallying cry and it was a huge battle in Congress,” Marshall says.

Naturalist John Muir led the fight against it. He wrote about the valley’s sheer granite cliffs and scenic waterfalls, calling it a twin to Yosemite Valley.

Eventually, he lost, and San Francisco began building the O’Shaughnessy dam in 1914 to collect water from the Tuolumne River. “Although they lost the battle, they launched a national environmental movement.”

Today the valley is under 300 feet of water, which supplies two and a half million people in San Francisco and cities around Silicon Valley. But the battle over Hetch Hetchy never really went away. In 1955, Sierra Club director David Brower made a film called “Two Yosemites.”

In 1988, the National Park Service released a study about what would happen to the landscape if the reservoir was drained.

“Within a year of the river reclaiming itself, you’ll start to see green meadows along the banks. And within a few years you’ll start to see saplings and trees come up,” Marshall says. Within 50 years, the report says, oak woodlands would return and pine trees would be 50 feet tall.

Of course, there’s the question of what happens to the water supply. Marshall says it can be stored elsewhere. “People mistakenly believe Hetch Hetchy is our only reservoir. It’s one of nine reservoirs. So what our initiative does is ask San Francisco to plan to consolidate from nine to eight reservoirs.”

Marshall says by expanding other reservoirs, using underground storage and recycling more water, San Francisco could make up for Hetch Hetchy’s storage. “We don’t recycle any water. We’ve stopped, for all intents and purposes, using groundwater, except for a little bit. Those are things we’re going to have to do anyway."

'Things Were Different Then'

“We are looking at recycled water. We are building recycled water plants. We are building groundwater pumping wells,” says Michael Carlin, deputy general manager of the San Francisco PUC.

The Tuolumne River emerges below the O’Shaughnessy dam.

“We’re looking at all those things. And to say, gee whiz, you also should just plan that your system is gone… doesn’t make any sense.” As a public employee, Carlin says he can’t take a position on the issue, but he has concerns.

The Hetch Hetchy system is reliable, he says. The water is so clean, it doesn’t require filtration. And the PUC doesn’t own all the reservoirs in the system, so Carlin says they’d have to rely on other water districts if the reservoir was drained.

“Asking them if they’re willing to store San Francisco’s water there, the answer that we’ve gotten from them at least is no,” says Carlin.

Then there’s the cost. Studies throughout the years have put it between one and 10 billion dollars.

The SFPUC has never studied it, but Carlin doubts that would help. “There have been extensive studies in the past. They have come to the same conclusion which is just a set of questions. And the issue is whether any additional study will just lead you to the same set of questions.”

The ballot measure has a number of opponents: San Francisco Mayor Ed Lee, Senator Dianne Feinstein and the Silicon Valley Leadership Group, who say it’s a huge risk, because businesses depend on reliable water.

“If we were to propose building this reservoir today in a national park, chances are it wouldn’t happen. But it happened in 1913. Things were different then,” Carlin says.

On November 6th, San Francisco voters will decide if they want to take a step toward rewriting that history.

Meet the Pika

The American pika lives at high elevations in the American West. Photo: Doug Von Gausig/Naturesongs.com

In a campground near Lake Tahoe, a group of seventh and eighth graders from West Oakland Middle School are sitting around a campfire, getting to know ecologist Joseph Stewart. And he's introducing them to his work. Stewart works with the California Department of Fish and Game and is a grad student at the University of Nevada-Reno, where he studies pikas.

"This is a picture of a pika," Stewart says.  He pulls out a photo and the campers click on their flashlights to see it.

"Ooh, they're cute," says seventh-grader Anisa Moore.

Pikas are related to rabbits. They're about the size of hamsters, with no tails and round Mickey Mouse ears. They live in rock piles at high elevations, and are adapted to cold temperatures. When it gets too hot, they hide out under the rocks. So Stewart is trying to figure out if pikas don't do well in the heat, what will happen to them as the climate continues to warm.

"They've been petitioned for listing under the Endangered Species Act because of climate change," he explains to the students. "But when the Fish and Wildlife Service reviewed that petition, they pretty much said that we don't know enough about how pikas are doing. We need more data."

Two years ago, the Obama administration decided not to protect pikas as endangered. But California is still considering it. If the state does decide to add them to its endangered species list, pikas would become the first species here to be listed as threatened primarily because of climate change. If the state starts protecting animals because of climate change, things that affect the climate, like new fossil-fuel power plants or clearcut logging projects, could be slowed.

The students are here with Howard Nathel, who volunteers at their school and organized the project.  They'll survey likely pika habitat, to help figure out where pikas still live, and in what locations they once lived, but don't anymore.

In the Wilderness

Fredrikka Lake at the border of Desolation Wilderness. Photo: Molly Samuel

To get to pika habitat, the students have to hike. Lake Tahoe isn't high enough for the cold-loving creatures.

They're heading to Tamarack Lake, a bright blue lake surrounded by granite and pine trees in the Desolation Wilderness near South Lake Tahoe. At about 7800 feet in elevation, it's in prime pika territory.

The next morning, Anton Jackson and Joe Green get their first glimpse of a pika as it scurries across the rocks.

"You guys see that?" Stewart points it out to them.

"Yeah," Jackson says. "It's right there. It's really small. It's on that little rock."

"That's hecka small," says Green.

The group that's leading this trip is Adventurers and Scientists for Conservation (ASC), a Montana-based non-profit. Usually the organization puts outdoor athletes — hikers, climbers, kayakers — in touch with scientists who study plants and animals in hard-to-reach places, like Mt. Everest, the Australian Outback or the Amazon.

This is the first trip the group has organized for students.

"It's such a cool way for them to have fun, to grow a lot, and to be excited about what it is to be a scientist," says Gregg Treinish, the founder of ASC. "And to have that idea in their heads that, 'Hey I can be a scientist. Hey, I can do this.'"

The students learn to take down the data they need: where they are, what time it is, and whether or not they found pikas. Stewart explains the best way to figure out if a pika lives — or has lived — in the area is by looking for pika pellets, which look like brown-green peppercorns. De'Jon Banks quickly finds some.

(From left to right) Brendan Weiner, Howard Nathel, De'Jon Banks, Fredrick Lake, Joseph Stewart, Anton Jackson and Joe Green look for pikas. Photo: Molly Samuel/KQED

"Oh, this pika poop right here?" He asks.

"Let's see. Looks like it. Looks like you found some," Stewart says. "So I'll write down that we found some…"

"Old pika poop," Banks offers.

This data will go into iNaturalist, a website where citizen scientists can upload their observations for scientists to use. This is the first time anyone's surveyed the area around Tamarack Lake for pikas.

Treinish says, this project isn’t just good for science, it’s also good for the students, who are going beyond pre-set lab experiments, and learning to do actual field work.

"They're in 7th grade from West Oakland, and they're going to be part of science, they're part of our scientific understanding of the world. And that's a really cool thing," he says.

Pikas in the Past, Present and Future

Later in the day, Stewart takes me to one of the sites he's studied. As it starts to cool off around dusk, the pikas emerge from under the rocks and begin calling. Their chirps bounce off the granite boulders.

"I don't think there will be pikas here in 50 years," Stewart tells me. "Right now it seems like there's tons, but if you change the climate, if it's on average a couple degrees Celsius warmer here, it's not going to be climaticly suitable for pikas."

Pikas have been moving uphill since the last ice age, to keep up with the cooler temperatures they've evolved to live in. As part of his research, Stewart searches for spots that would be good pika habitat if they were higher and cooler. When he finds pika pellets in those locations, he can tell they once lived there.

As the climate continues to warm, their range will get even smaller. Stewart says anthropogenic climate change means, they may disappear from Northern California entirely.

Pika Policy

The more scientists know about their numbers, the better informed government leaders will be when deciding whether to classify them as endangered.

The California Department of Fish and Game is expected to recommend whether or not to list the pika as threatened later this year.

West Coast scientists are studying how California mussels might adapt to ocean acidification.

This week, scientists from around the world are meeting in Monterey to discuss what they call the “other” climate change problem: the oceans are becoming more acidic. It happens as oceans absorb the carbon dioxide we add to the air through burning fossil fuels.

Scientists say it can be bad news for ocean animals with shells like oysters, mussels and others that are key to the marine food web. How bad? Some scientists are hoping that ocean conditions off the California coast will help them find out.

Oyster Farms Face Impacts

You don’t have to go far to see the impacts that acidification is already having. At Hog Island Oyster Company, just outside Point Reyes, co-owner Terry Sawyer is seeing the effects in his supply chain.

The oysters grow up in big, mesh bags that sit out in Tomales Bay, but Sawyer gets the oysters when they’re small, “the size of your little fingernail,” he says. He orders them from hatcheries in Oregon and Washington.

A few years ago, Sawyer started getting calls from those suppliers. They couldn’t fill his orders.
“They would have tens of thousands of gallons of tanks that were absolutely full of larvae. They would have the entire system die or crash,” says Sawyer.

A pile of oysters being sorted at Hog Island Oyster Farm.

The hatcheries were filling their tanks with seawater that was becoming more acidic. Scientists say the oceans are 30 percent more acidic since the start of the Industrial Revolution.

The more acidic the water, the harder it is for animals like oysters to build their shells. Their shells are weaker and they grow more slowly.

Sawyer is raising his own oyster larvae now so he’ll have a more predictable supply. But he says there’s no question that climate change is affecting his bottom line.

“We don’t know if we’re going to be able to survive the very real trending that is going on out there," he says. It’s a trend that could affect the entire food web.

Acidification on the California Coast

“You can see here, this is a mussel bed that’s made up of lots of California mussels,” says Eric Sanford, an ecologist with UC Davis’s Bodega Marine Lab.

The rocky point we’re standing on is covered in tightly packed, purplish mussels – what he calls the “foundation species” of the California coast. “One that really defines the whole ecosystem, sort of the way corals define a coral reef,” he says.

Mussels are a key part of the food web and so are a lot of animals with shells, says oceanographer Tessa Hill. “Probably most people like the fact that we have things like whales and salmon off along our coast. Those organisms are likely to be impacted because their food source will be impacted,” Hill says.

The big question is: will animals with shells be able to adapt to a more acidic future – where, in a hundred years, the oceans could be more than twice as acidic?

Eric Sanford at a mussel bed near Bodega Marine Lab.

These California mussels could help answer that.

“They’re facing the most acidic water that you’d see in the open ocean today,” says Hill.

As Hill explains, acidic water from the deep ocean rises to the surface on the West Coast in the spring and summer, when the wind is blowing. This upwelling makes the waters off California some of the most acidic in the world.

As part of OMEGAS, a new project linking universities up and down the West Coast, researchers are asking: if organisms here have been blasted with more acidic water for generations, have they adapted to handle it?

Inside their lab, Hill and Sanford show me jars full of young mussels, almost too small to see. Each jar is from a different part of the West Coast from Oregon to Santa Barbara. They’re being grown in water that reflects conditions in 2100, says Eric Sanford.

“The issue we’re looking at is whether there might be genetic differences among different populations along the coast in their ability to cope with ocean acidification,” he says.

Finding Genetic Tools

“We found they have lucky genes,” says Steve Palumbi, biology professor at Stanford University who is also working on the OMEGAS project. He studied populations of another shelled animal on the West Coast – sea urchins.

You can think of genes like a set of tools, he says. “If you happen to have bad plumbing, you will have more plumbing tools in your house.”

There have been lots of plumbing problems on the West Coast, so to speak, in the form of acidic water. “And so all these populations, urchins anyway, have had to get the toolset to deal with it,” says Palumbi.

In a paper still in review, Palumbi says they found a segment of the urchin population that had around 100 genes that make them better adapted to more acidic water. That makes them more likely to survive and reproduce. (Check out this microdoc video for more on their research).

“This is good news,” he says, “because these organisms have the capacity to deal with more acidification. But it’s not good news forever because all it does is give us a little breathing room. The trouble is right now, the rate at which the ocean is acidifying is way faster than it ever has before.”

Organisms will evolve, he says, but probably not fast enough to keep up. In the meantime, Palumbi and other scientists are mapping where the genetically resilient mussels and urchins are on the West Coast, so policymakers can look at protecting them.

The space shuttle Endeavour logged 122 million miles over its 20-year career.

Friday morning’s journey will add a final thousand or so as the shuttle makes its way from Edwards Air Force Base in Southern California, up to the Bay Area, then down toward Los Angeles.

The Endeavour flyover will make for a striking sight: piggybacked to a 747, the shuttle will be flying at a low altitude of 1500 feet in some parts of the Bay Area.

Chabot Space and Science Center in Oakland is opening its doors at 8AM for a viewing party, says the center’s Ben Burress.

“Fifteen-hundred feet, coincidentally is the altitude here at Chabot, so we expect to see a very good side view,” he says.

Bay Area residents will get their best views around 9:30 AM, as the shuttle crosses the Bay toward the Golden Gate Bridge and Crissy Fields, then heads down the peninsula toward Los Angeles.

The End of an Era

Friday’s trip marks the end of an era, not just for the Endeavour, but for NASA’s entire space shuttle program, which was conceived in 1972 and ultimately put five shuttles into space.

NASA's shuttle program aimed to made space a place astronauts didn't just visit occasionally, but actually worked.

Just three years after putting a man on the moon, NASA's Space Shuttle program envisioned a series of reusable, utility-scale workhorses.

Endeavour was exactly that, says Burress.

“Some people described it as a large pick up truck,” he says. “Its vision was that it would be able to take large satellites and other equipment into lower-earth orbit.”

The Endeavour replaced the Space Shuttle Challenger, which exploded just after takeoff in 1986, killing seven astronauts.

Between 1992 and its final trip in 2011, the Endeavour ferried pieces of the International Space Station and the Hubble telescope into place and fixed a malfunctioning communications satellite, among other missions.

Endeavour will spend its retirement at the California Science Center in Los Angeles.

For Burress, like most people, Friday will be the first – and last – glimpse of a space shuttle in the air.

“Probably from now on, we’ll only see them on the ground,” he says.

Mice bred with a Slitrk5 mutation groom themselves compulsively. Video still courtesy of Nature and Francis Lee

The field of psychiatry is going through major changes this year. For the first time in almost two decades, the Diagnostic and Statistical Manual of Mental Disorders, or DSM, as people in the field call it, is getting an overhaul.

Among the proposed changes: a new category called Obsessive Compulsive and Related Disorders. It would include not just OCD, but other, more common, disorders, including one I know all too well.

I’m a nail biter. And I can tell you the exact moment I became one. I was six years old, watching my mom get dressed for work. As she paused to mull something over, she chewed on the nail of her index finger. How cool! How grown-up, I thought. I think I’ll try it.

I never stopped. In fact, for 30 years, I bit them to the nubs. It was embarrassing. For me, it’s like wearing your neuroses on your sleeve. At parties, I learned to wrap my fingers all the way around my wine glass, so that my nails faced my chest. I hated filling out forms in public places.

Then, recently, something happened that made me finally quit biting my nails. I’ll get to that in a bit.

But I was feeling pretty pleased with myself when I spread my hands out in front of Carol Matthews. She’s a psychiatrist at the University of California San Francisco.

"Pathological Grooming"

“Well, I can see you’re a nail biter,” she told me. Your cuticles are pushed back and you have the bumpiness you see with chronic nail biters. But it’s not bad. It looks like you’re a recovered nail biter, is what I’d say.”

Matthews specializes in pathological grooming, a group of behaviors that includes nail biting, although nail biters rarely come in for treatment. She says the patients she sees the most are the trichotillomaniacs, people who pull their hair out.

“Trichotillomania is the most socially visible,” says Matthews. “It's much harder to hide the fact that you don't have eyebrows or that you have a big bald spot, so it’s much more distressing to people. Skin picking comes next.”

In a sense, these behaviors stem from a normal, evolutionarily adaptive behavior: grooming. But in pathological groomers, those behaviors go haywire. Instead of being triggered by, say, a hangnail, a pathological nail-biter will be triggered by all sorts of things: driving, reading a book, or feeling anxious.

From "Not-Otherwise Classified" to "Obsessive-Compulsive Spectrum"

Until recently these pathological grooming behaviors were classified almost as an afterthought in the DSM: “Impulse-Control Disorders Not Otherwise Classified.”

But the new DSM, the DSM-5, proposes something different.

It creates a category called Obsessive Compulsive and Related Disorders that includes classic OCD behaviors, people who wash their hands compulsively or have to line up their shoes a certain way. The idea is to expand this group so that it includes not just OCD, but pathological grooming, as well as hoarding and several other disorders.

This does not mean that insurance companies are going to raise premiums on nail biters, or issue policy-mandated manicures. (In fact nail biting, itself, isn’t even specifically mentioned in the DSM-5, because in the vast majority of cases, it’s not disabling enough to count as a “disorder.”)

But the new classification does give nail biters – and psychiatrists – another way to think about something that used to be considered simply a bad habit. And that raises some questions.

For one, says Mathews, “There’s always the worry of are we over-pathologizing normal behaviors. That’s always a worry with the DSM.”

And does this grouping make sense?

Nail biting? It's a little bit fun.

After all, there are real differences between OCD and those of us who pick, pull, or bite, including one big one.

“In OCD,” says Matthews, “the compulsion is really unwanted.”

People with OCD don’t want to be washing their hands, or checking the stove over and over again, she says. They’re terrified that if they don’t do it, something bad will happen.

But the biters hair pullers and skin pickers? They tell a different story. Matthews says she hears this from her pathological groomers all the time: They enjoy it.

“It's rewarding. It feels good,” she says. “When you get the right nail, it feels good. It’s kind of a funny sense of reward, but it’s a reward.”

Another consideration for the drafters of the DSM-5, when cataloguing all these disorders, is genetics. Are there genetic signatures that help explain both OCD and pathological grooming? Do the two behaviors share any genetic markers? And to what extent are these behaviors hereditary?

Meet the OCD mouse

Francis Lee is a neuroscientist at Weill Cornell Medical College in New York. He studies mice.

A few years ago, a colleague – another mouse guy — came to Lee with a mystery: a mouse, bred with a specific gene mutation, that was behaving very oddly.

“I was dumbstruck,” he says.

The mouse was doing something Lee instantly recognized from his work as a psychiatrist, studying people.

“It was hunched over,” Lee says, “repetitively moving its front paws over its eyes and ears.”

In mice, as in many animals, such grooming behaviors are normal and healthy. But these mice were doing it at a completely different scale. Whereas normal mice might groom themselves for a couple of seconds, mice with this genetic mutation – the Slitrk5 deficiency – groom in bursts of 30 seconds or longer, then start all over again just seconds later.

In fact, the mice groom so much, they give themselves bald spots.

“They remove the hair from around their eyes. They actually look like they have little white rings around their eyes,” says Lee

To Lee, who published this work in Nature Medicine in 2010, this mouse-brand of pathological grooming looks like OCD: a repetitive behavior that the mice are compelled to do. And just like people with OCD, these mice, he says, often exhibit high levels of anxiety and fearfulness. In fact, they’re some of the most fearful, risk-averse mice he’s ever seen.

Lee’s work shows that in mice, a single gene tweak can cause OCD-like symptoms, including over-grooming. Now, scientists are trying to find out whether the same mutations might contribute to OCD, or pathological-grooming, in people.

The (bitten) apple never falls far from the tree

Which brings me to the reason that I finally quit. My daughter Cora, age 3, recently started biting her own nails.

When I asked her about it, she explained, “I don’t want to put my fingers in my mouth. I just do it even though I don’t want to.”

I felt terrible about this. Either I’d waited too long to stop biting my nails and Cora had learned from watching me — the same way I had, with my own mother — or I'd passed on some pathological grooming gene that had her doomed from the start.

Worse, I was making her feel bad about it.

“I’m gonna stop doing it,” she told me. “Why?” I asked. “Because you don’t like me to, remember?" she replied.

In many ways, these questions the DSM is grappling with are the same ones we parents have about our kids. Are our genes their destiny? What’s a bad habit, and what’s a pathology?

The newly revised DSM-5 will be released in San Francisco in May 2013. Maybe around the time Cora’s own kids start biting their nails, she’ll have better answers than we do now.

Lettuce plants genetically engineered to withstand heat

Proposition 37 could make California the first state in the country to require labels on foods made with genetically-modified ingredients. It’s shaping up to be one of the most contentious — and certainly the most expensive — battles on the state’s November ballot.

On one side are organic food groups that have spent about $3 million in support of the labeling law. On the other are biotech firms like Monsanto, and food giants like Pepsi, Sara Lee, and General Mills, which have contributed upwards of $28 million to try and keep GMO labels off food packages.

If Proposition 37 passes, you’ll see a change in nearly every part of the grocery store.

Take the cereal aisle, where Stacy Malkan with the "Yes on 37" campaign recently picked up a box of granola and pointed to the ingredients panel.

“Many of these products have corn syrup, cornstarch, sugar beets, and soy products that are genetically engineered," she said.

In the United States, up to 90 percent of those foods are grown from seeds that have been genetically modified. Scientists made changes in the plants’ DNA to make the crop, for example, resist pests, or stay fresh longer.

Malkan thinks that's something consumers should know about.

Would labels inform people? Or scare them?

“It's not a warning sticker,” she says. “[it’s not] a skull and crossbones or anything. It's literally just a few words added to existing labels, just indicating [the food was] partially produced with genetic engineering.

But to the "No On 37" camp, there is nothing benign about a label.

Take, for instance, Kent Bradford, a professor of plant science at the University of California, Davis, and director of its Seed Biotechnology Center.

Bradford's team works with, among other plants, lettuce.

Kent Bradford directs UC Davis's Seed Biotechnology Center

California supplies 80 percent of the nation's lettuce. But growers here, he says, increasingly find themselves at odds with a fact of nature.

Lettuce, he says, evolved for a Mediterranean climate. Its seeds lay dormant when it’s hot, and germinate when it rains.

But it’s getting hotter here in California. And farmers want to be able to grow lettuce year-round, not just when it rains. So Bradford’s team is developing a new kind of lettuce seed.

He points to several strands of straggly, stringy lettuce. At this overgrown stage, it's not appetizing-looking produce. But Bradford says these plants could help farmers adapt to a changing climate.

"What we've identified here is if we turn off this one gene, it eliminates that mechanism of inability to germinate at high temperature," he says.

GM isn't an ingredient, it's a technology

Part of what bothers Bradford about Proposition 37 is that genetic modification isn’t an ingredient, like saturated fat. It's a technology, one capable of creating countless variations on nature, some of them potentially very useful.

Genetically-engineered lettuce can sprout in a hot, dry climate.

"You wouldn't want to label a screwdriver as dangerous just because someone might poke it through their hand or something."

Bradford fears that if Prop 37 passes, consumers will regard those GMO label as a scarlet letter, a signal that the entire technology is flawed and dangerous.

"Why would they be putting this on the label if it weren’t something I should be concerned about?"

Indeed, that's the question many consumers have about genetically modified foods: Are they safe?

Is GM safe? Grappling with a scarcity of science

Unfortunately, the body of peer-reviewed research on GM foods is tiny, consisting of a handful of small studies done on mice. Some of these studies suggest possible links to immune-system impairment and other problems. Compared to the amount of research done on, for instance, BPA, it's a drop in the bucket.

Both the American Medical Association and the FDA say that genetically-modified foods are safe to eat and do not need to be labeled.

But Prop. 37 advocates and critics of GM foods say the fact that the science is nascent only underscores the need for greater regulation and labeling.

They say the process of genetic engineering can be imprecise, and that plant scientists may not always know the full, long-term implications of the crops they develop.

"The jury is still out on the health effects," says Yes on 37's Stacy Malkan. "And in many ways, the evidence hasn’t even been presented."

Such concerns are widespread in Europe, where GM labeling is mandatory. But that's also increasingly the case in California, where a recent poll found 65 percent of voters planning to support Prop. 37.

Here in the states, at least, it wasn't always this way.

We've been here before: The lesson of the Flavr Savr tomato

Belinda Martineau was a plant scientist at the Davis-based biotech firm Calgene in the late 1980s and early 90s. She was part of the team that helped invent the Flavr Savr tomato, the world’s first commercially-available genetically modified whole food.

Martineau says she and others at Calgene weren't sure how the Flavr Savr was going to go over with the public.

"Jurassic Park came out while we were readying the tomato for the marketplace," she recalls. "We were worried about it. We were worried about the public’s perception."

Belinda Martineau helped develop the Flavr Savr tomato

So Calgene made a choice: total transparency. The Flavr Savr wasn’t just labeled, it came with a brochure shaped like a tomato.

"It actually explained the genetic engineering technology in lay terms that people could understand," "And it had a 1-800 number, in case people wanted to learn more."

No laws required that Calgene label the tomato. Martineau says the company wanted to label the Flavr Savr because they were proud of it.

"We wanted to be transparent"

"We believed in what we were doing. We thought if we were careful about it, and transparent, that we could convince the public that they should be as enthusiastic about it as we were."

And shoppers were enthusiastic. In Davis, where Martineau lives, Flavr Savrs flew off the shelves.

"They had a policy at the local IGA that you could only purchase two Flavr Savor tomatoes per person, per day," says Martineau. "How they kept track of that, I don't know."

What ultimately killed the Flavr Savr wasn't the public’s fear of genetic engineering. It was the technology itself. Flavr Savrs didn’t taste better than regular tomatoes and they were too difficult to transport.

For Martineau, there’s a lesson here. Not labeling, she says, makes the industry look like it has something to hide. She believes labeling is an opportunity.

"This is one of the best ways the industry can turn public opinion around, is to be honest, to be transparent. And to come out and be proud of their products."

If Proposition 37 passes on November 6, the question is whether the public will see those labels the same way Martineau does.

Climate change could dramatically affect the microclimates that have made California wine country so successful.

You've probably heard of the wines that made Napa and Sonoma famous, like Cabernet Sauvignon or Chardonnay. But what about Negroamaro or Nero d'Avola?

They're wine grapes that are well-adapted to hotter climates – the kind of conditions that California may be facing as the climate continues to warm. But for wineries that have staked their reputations on certain wines, adapting to climate change could be a tough sell.

Talk to any wine lover in California and they'll tell you how lucky they are to live in such rich wine-producing region. Take the recent meeting of the San Francisco Wine Lovers Group at Toast wine bar in Oakland, where the favorites are California Pinot Noir, Russian River Zinfandel, and Napa Cabernet.

In fact, the type of grape – or varietal – is how most of us think about wine.

"That's the big problem," says Andy Walker, a grape breeder in Viticulture and Enology at the University of California-Davis. "We've spent the last 100 years emphasizing varieties and we've really marketed those names very effectively."

Walker is strolling through UC Davis's test vineyard, where hundreds of different wine grapes from around the world are grown. The vast majority are unknown to consumers, because most wineries focus on only a handful of grapes. "Chardonnay, cabernet, merlot, pinot noir – those would make up probably a large percentage," he says.

Those are all French varieties, mostly suited for cool climates. California is warm by comparison and thanks to climate change, it's expected to get a lot warmer. Extreme heat can be the enemy of good wine. "It destroys acidity primarily and it changes color and aromatics," says Walker.

According to a recent study from Stanford University, about two degrees of warming could reduce California's premium wine-growing land by 30 to 50 percent. That could happen as soon as 2040. Water supply is also expected to be an issue.

"I think the interesting thing for me as a breeder is to take advantage of this and say, OK, here's a chance now to change thought and let's actually readapt varieties to California," he says.

Andy Walker walks through UC Davis's test vineyard.

But in many circles, grape breeding is a dirty term, according to Walker.

"Viticulture is the most backward form of horticulture that exists. We use these varieties that haven't been changed for decades, for millennia in some cases. And it really doesn't make any sense."

The problem starts in today's vineyards. If you look at rows of Pinot Noir vines, you aren't just looking at the original varietal. You're looking at clones. That's because vines are grown from a branch that's taken off an existing plant.

"Pinot noir is being propagated year after year after year. This essentially means that grapes have not been having sex very much," says Sean Myles , a geneticist at the Nova Scotia Agricultural College.

He says breeding is key for other crops, since farmers need seeds to plant every year. Wine grapes miss this opportunity to develop adaptability and disease resistance, since vines don't grow from seeds

"That means that we're not allowing the genetic material to be shuffled anymore. That genetic material is now standing still in time. And while the pathogens are evolving, the pinot noir is not," says Myles.

Andy Walker says there's plenty of genetic diversity out there for breeding, if you wanted to make today's varieties more heat tolerant or drought resistant. But there's a very big problem. Once your breed your pinot noir with something else, you can't call it pinot noir anymore.

"The last decision that hardest. Can we market this variety? We know it produces exceptional wine. We know the quality is better. But the next step is can we actually market it," says Walker.

That's a deal breaker for many vineyards, who think consumers won't buy varieties they don't recognize. Walker says looking ahead to climate change, there are already varieties out there today from Italy and Spain that would do well in a warmer California. "We could produce Barbera instead, or Negroamaro or Nero d'Avola from southern Italy and we'd be far better ahead."

These lush reds are popular in Italy but not so well known to Californians. Walker says it'll come down to marketing. "I don't think it's the consumer that's gonna make the shift. They have to be directed."

"I think it's really a pull from consumers," says Nick Dokoozlian, a Vice President at E & J Gallo Winery, the largest family-owned winery in the US. "In most cases, we're responding to consumer demand for a cultivar."

Dokoozlian says Gallo has been testing new wine varieties throughout its vineyards and has found some promising grapes. "The problem is we can't necessarily sell those varieties. Consumers aren't aware of them. The marketing aspect of climate change and the adaptation to climate change, really, the hurdles on the marketing side are much, much more significant."

Since vineyards can last up to 30 years, he says switching varieties is a major financial gamble. "The wine business is an extremely capital intensive business. The financial risk of planting the wrong variety in the wrong place is pretty significant."

Still, given the temperature and water supply changes projected for California, Dokoozlian sees the market shifting eventually. "I'm looking forward to having world-class California Nero d'Avola soon."

One of Google's self-driving cars. (Image: Google)

It’s every commuter’s dream – you’re stuck in an epic traffic jam and with the press of a button, your car does the driving for you. Now, thanks to companies like Google, robotic car technology isn’t far off. This week, the state legislature is considering a bill that would set up rules for putting self-driving cars on the road.

The technology has evolved rapidly. Just five years ago, I was in an empty parking lot in Mountain View, taking a ride in what was once an extremely rare vehicle.

“We’re seeing a 3-D rendering of Junior’s understanding of the world. So you see the car, but around the car you see the sensor data,” said Mike Montemerlo, pointing to a laptop screen. At the time, he was an engineer at Stanford University working on Junior, the robotic car. I was tagging along on one of Junior’s test drives.

“We’ve parked this Tuareg in the way here so he has to maneuver around it to fit into his parking spot,” he said. Using lasers mounted on all sides of the car, Junior avoided the other car and swung into a parking place, its steering wheel turning back and forth independently.

Junior had a lot in common with a teenage driver. “He’s still not very smooth, but we hope he’s reasonably safe,” said Montemerlo at the time.

What a difference five years can make.

“We just announced that we’ve driven over 300,000 miles without incident while the cars in are autonomous mode,” says Leslie Miller, public policy manager at Google.

The company has driven away with robotic car technology, so to speak. Google has a dozen of these cars and for the past few years, they’ve been testing and tweaking them. “The vehicles have been on highways, in congested urban streets. We’ve been down curvy roads including over the Santa Cruz Mountains,” she says.

Someone’s been in the driver’s seat for all those test drives, just in case. But the cars are in sort of a legal gray area. “No state in the country built rules of the road with the idea that autos would be able to operate without a driver behind the wheel. So we want to help establish these parameters,” says Miller.

That’s why Google is sponsoring a bill in the California Legislature that would allow self-driving cars on the road. It also instructs the DMV to set up safety standards for the cars. That includes things like: if the car’s computer crashes, it comes to a complete stop.

A Google car with a special Nevada license plate. (Image: Nevada DMV)

Nevada and Florida have already passed similar bills and earlier this year, Nevada was the first state to officially license Google’s self-driving Priuses. The cars were given special red license plates. Miller says they’re hoping to see the legislation spread nationwide.

“For Google, the interest is reducing the number of accidents and fatalities that are caused by human error on the road. The technology is not going to be distracted by grabbing the phone or eating lunch or putting mascara on,” says Miller.

Google hasn’t said what its business plan is for the technology, but many in the industry expect fully self-driving cars to be available in showrooms as early as 2025. That raises a host of legal issues.

“In California, the biggest issue right now has to do with liability,” says Daniel Gage, spokesman for the Alliance of Automobile Manufacturers.

Gage says while a lot of car companies are developing their own autonomous technology, they’re opposing California’s self-driving car bill over legal concerns. If one of these cars crashes itself, automakers don’t want to be held responsible when a third party like Google installs the technology. “This is a big issue for automakers. It always has been and it probably always will be.”

“Eventually there will be incidents and there will be litigation,” says Bryant Walker Smith, fellow at Stanford Law School. Privacy groups, he says, are concerned about the personal data these cars might record, since they clearly know where you are.

Then there’s the question of how tough safety standards should be. “Should these vehicles be expected to drive perfectly without any collisions ever? Should they be expected to perform as well as a perfect human driver or an average human driver or better than an impaired human driver?” says Smith.

Even trickier are cases where we make moral decisions as drivers. “Say if a vehicle has to choose between hitting a child in the street or swerving and going off of a cliff. That’s a decision that someone would make in the spur of the moment. Do they save their life or somebody else’s? What decision would a vehicle make and who would be responsible for making that decision?

If these seem like heavy issues for a state agency to figure out, Smith says there will be a transition to self-driving automobiles. Automakers have already rolled out technology that warns drivers about their blind spot and helps them avoid accidents.

Despite the questions that remain, the impact, says Smith, will be huge. “Our existing world is one in which 30,000 people die in the United States on the road every year. Drivers who are impaired or unqualified are behind the wheel. I would ask is the status quo acceptable?” he says.

If the California Legislature passes the self-driving cars bill, the Governor has until September 30th to sign it.

Here's a video from Google showcasing their technology:

UC Davis's Roger Chetelat holds a few "square tomatoes."

Decades ago, researchers figured out how to create the picture-perfect tomato that travels well and is available year-round. The trouble is, as any supermarket shopper can tell you, tomatoes that look great sometimes taste terrible.

It’s not hard to see how much some tomatoes have changed. Just take the trucks on California highways during the summer, each pulling a double trailer stacked high with tomatoes. There’s a reason the tomatoes at the bottom of the pile aren’t squished into a tomato-y mess. That's thanks to the square tomato.

“The square tomato is kind of a misnomer,” says Roger Chetelat, director of the Tomato Genetics Resource Center at the University of California-Davis. We’re in a greenhouse on campus where he’s holding a few square tomatoes.

“You can see they’re not square but they are blocky,” he says. The tomatoes are sort of flat on the side and are firm to the touch even though they’re ripe, sort of like a baseball. “I think I’d prefer to have a tomato like that thrown at me than a baseball, but yeah, they’re pretty tough,” Chetelat says.

Fifty years ago, farmers were looking for tougher tomatoes that could withstand new mechanical picking machines. So, plant breeders at UC Davis created a tomato with thick skin and a firm, meaty inside. California’s tomato production boomed.

Unintended Genetic Consequences

But the era of modern plant breeding came with some unintended effects, as UC Davis researcher Ann Powell discovered.

She demonstrates with a genetic taste test, of sorts. “We can try one of these,” she says, cutting up a standard grocery store tomato. “Tastes tomato-y.”

Young tomatoes with green shoulders on the left and no shoulders on the right.

The other one we’re sampling has what Powell calls “green shoulders.” That means, as it grew, the tomato was dark green on top around the stem – something that’s controlled by a specific gene.

“They’re sweeter,” Powell says, tasting it. “Whether it’s all due to that particular gene, I can’t tell you. But, I don’t know, you can taste the difference.”

If green shoulders don’t sound familiar, that’s because most commercial tomatoes don’t have them anymore. Seventy years ago, breeders selected for uniformly light green tomatoes with no shoulders, which stood out better against the plant’s dark leaves.

“They’re a lot easier to see so a farmer could judge his yield. They could see how productive the plants were a lot easier,” says Powell. Their uniform color was also more attractive to consumers.

It turns out, those green shoulders have a key job. “We found that it influences the amount of sugar in the ripe fruit,” she says. The dark green parts have more chloroplasts, which turn sunlight into sugars.

“It made about a 20 percent difference in the amount of sugars. I think of it a little bit like how you eat berries. Most of us, including me, sprinkle a little bit of sugar on top to sort of enhance the flavor,” says Powell.

Ann Powell looks at tomatoes in a UC Davis greenhouse.

Most heirloom tomatoes still have green shoulders, but Powell says now that they know about this gene, plant breeders could put it back in commercial varieties. And since the tomato genome was sequenced earlier this year, there are still other flavor genes to study.

Focusing on Taste and Nutrition

“We’ve modified and changed our food radically,” says Alyson Mitchell, professor in UC Davis’s Food Science and Technology Department.

“We’ve bred these seeds and plants to have all of these other characteristics: uniform shape, size, color, good disease resistance, high yield,” she says. That’s had major benefits: produce is widely available and more affordable.

On the other hand, “we’ve absolutely not paid attention to flavor and nutrition. You know, we’re telling children, eat more fruits and vegetables at a time that fruits and vegetables have never tasted worse,” Mitchell says.

Scientists are just starting to understand the molecular compounds that control taste and nutrition. “What we do know is that not all tomatoes are the same. Different cultivars have different levels of nutrients in them,” she says.

Growing them organically can also change the levels of nutrients. In a ten-year controlled study of tomatoes, organic tomatoes showed higher levels of antioxidants and molecules that make up flavor and color. But researchers still aren’t sure which of these compounds are the most important for our health. Take flavonoids, which have gotten a lot of hype as antioxidants.

“There are about sixteen hundred described flavonoids to date and we don’t even really at this point understand what that complement is, let alone what all of those different compounds do to benefit our health,” Mitchell says.

Even if there is one nutrient that stands out, it’s not always easy to enhance it. Take the case of “super broccoli.” “So they made this broccoli and the idea was to market it as a super broccoli because it had very high levels of this antioxidant, quercetin. Well quercetin is really bitter and they sat a bunch of people down to eat and nobody could eat it, it was so awful,” says Mitchell.

Mitchell says it’s probably the combination of nutrients that gives produce its punch, which they’re working to understand better. Until then, she says, there is one way to make sure you’re getting those benefits: follow your mom’s advice and eat more fruits and vegetables.

BMW's production convertible. Photo: Joshua Cassidy

Americans spend much of their time sitting in two places: behind the wheel of their cars and in front of their computer screens. So it makes sense that Detroit auto companies and Silicon Valley technology companies would eventually try to figure out how to combine these two key parts of American society. As Andrea Kissack reports, putting Internet access in cars may be the ultimate in mobile technology, but it comes with a host of opportunities as well as dangers.
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A Smart Phone on Wheels

It’s a sunny day in San Francisco’s Mission neighborhood. I am taking a spin with Rob Passaro, the head of BMW’s app center in Mountain View. We’re driving a shiny red BMW convertible, it’s a test car–loaded with some of the car maker’s latest high-tech entertainment features.

“Here we are driving the streets of SF, and let’s say I really would like to hear some of my favorite music," says Passaro. "Luckily I’m a Mog subscriber.”

Hungry? BMW's iDrive system allows users to access popular features such as Yelp. Photo: Joshua Cassidy.

Passaro snaps his iPhone into a cradle between the front seats and uses a rotating knob down by his gear shift to control his infotainment choices, which are displayed on a screen in the dashboard. The car is now recognizing one of his phone’s music apps.

“ [It's] streaming through the iPhone and heard through my audio system in the car,” explains Passaro. An acoustic Fleetwood Mac song soon fills the cabin.

“I think the best way to think about it is the automotive screen is really like a fourth screen. You have TV, you have your laptop, you have mobile, you have automotive,” says Passaro.

While many drivers already use things like Bluetooth technology to sync their phones with their cars to make telephone calls, this is different. The smart phone connects to BMW’s iDrive system, an onboard computer with internet capability that allows drivers to access features like news, music, Yelp and email – all of which are already programmed into the car. Drivers also can access a number of third party apps through a plugged-in internet-enabled device.

As Passaro puts it, it’s a smart phone on wheels.

And what’s a smart phone, without access to social media? Like several car companies, BMW offers a feature, in its newer models, that displays as well as reads, Facebook and Twitter updates through a connected iPhone.

Next summer BMW will be integrating into its electronics system the velvet-toned voice of Apple’s Siri. Passaro says BMW has worked hard to establish relationships with big tech companies.

“We are finally playing in the same realm as the Apples and the Googles," he says. "We can play with them so we think a lot of good things can come out of that.”

Ford and Hackathons

Since BMW established a presence in Silicon Valley well over a decade ago, several other auto makers have made the move to tap into the area’s tech innovation. Julius Marchwiki is Global Product Manager for Sync App Link at Ford.

Ford's SYNC technology in the 2012 Ford Fiesta (image provided by Ford Motor Company).

“Being in Silicon Valley really brings app developers to your door,” Marchwiki says.

Ford opened a research office in Palo Alto earlier this year. Ford engineers already have held two “hackathons” – intense brainstorming sessions with Facebook app designers.

One of the first use cases Marchwiki says he saw with the group of hackathon members was the concept that since they are all in this younger age group, (we can use) planning events on Facebook.

"And we mention that we used to get into our cars. We knew we had some place to be, we didn’t know exactly where to go," he says. "So that was one of the first things we explored was – is there a way to start linking these great Facebook services into your navigation system?”

Driver Distraction

Ford is exploring ways to integrate Facebook into its voice controlled Sync system, Marchwicki says the company is trying to find the right social media apps that are both useful to drivers and safe. With the increasing number of in-car electronics you can guess that driver distraction is becoming a big concern.
Some of the new features are just too tempting, take for instance the dashboard display on Tesla’s new Model S. The Silicon Valley-based electric car maker is offering a screen nearly the size of two iPads, with a built in web browser that shows high definition videos, maps and web pages. Some sobering facts, though, the CDC says more than 1200 people are injured and 15 die each day in crashes in the U.S. due to distracted driving.

The 17-inch center panel screen on Tesla's Model S lets the driver control everything from navigation to basic web browsing (photo by Flickr user pkingDesign).

California is ahead of most states. It already has laws on the books that ban hand held texting as well as surfing the web from a display screen while driving.

"The government has to play a role to guard and watch what’s happening in this space," says Thilo Koslowski, a senior analyst with the technology research company Gartner. "Ultimately it’s the users fault, but the manufacturers have the responsibility to create these systems and educate consumers on when they can use them and what the risks are involved in this."

Thilo Koslowski has been looking at the convergence of technology and cars for fifteen years.

"There is a hype shaping up with the automotive industry," he says. "I see more and more of what is happening today does not need to be translated to the vehicle. They are just trying to copy and paste it into the vehicle, such as mobile services focused on social media."

Koslowski’s company has surveyed consumers and found that most are not so interested in keeping up with tweets while in the car. He says they want more road data through enhanced navigation and hands-free phone service.

"Similar to ten years ago, phones became smart phones. We are seeing the same transition now with automobiles where we are getting from basic transportation to intelligent mobility," Koslowski says.

Koslowski believes by 2016 most consumers will expect smart phone integration in cars and he says this is just the beginning of the connected drive. He expects that soon we will be using apps to connect to large amounts of data stored online that could include our cars' maintenance records, road conditions and traffic information generated from other cars.

Late Sunday night, scientists at NASA’s Jet Propulsion Laboratory in Pasadena cheered as the Curiosity lander ended its 352 million-mile journey, arriving – intact – onto the surface of Mars. The nail-biting landing procedure had been called the “Seven Minutes of Terror,” based on how long it took the lander to cut its speed from 13 thousand miles an hour… to zero.

For scientists at NASA Ames in Moffet Field, the work is just beginning. NASA Ames senior scientist David Blake designed CheMin, one of the scientific instruments that hitched a ride to Mars aboard Curiosity. CheMin, short for Chemistry & Mineralogy, uses x-ray diffraction to analyze soil and rock samples that the nuclear-powered rover will collect as it explores the Martian surface.

That data, which will be transmitted back to Earth, may help scientists solve one of the Red Planet's most compelling mysteries: whether water once flowed over its now-parched surface.

The mission is expected to last two years, but could go on much longer, depending on Curiosity’s life span. The lander can meander up to 12 miles over the Martian surface, with a speed limit of about 300 feet per hour. All the while, Curiosity’s 17 cameras are designed to stream images back to Earth of what it finds.

KQED News anchor Joshua Johnson spoke with NASA's David Blake just hours after the landing.

Johnson: Good morning!

Blake: Good morning.

Johnson: Congratulations, first of all. I’m sure you were up all night watching the landing.

Blake: Well, yeah, to say it was exciting is an understatement. You know once the vehicle hit the atmosphere of Mars, and things went so fast, it was almost like your brain couldn’t follow, and when those first thumbnails came down, it was just pandemonium. Everybody just erupted and started screaming and hugging each other.

Johnson: I imagine that seven minutes started to feel like seven seconds as the time slowed down.

Blake: It was amazing, and the control room was live saying ‘OK the heat shield has been released. OK the parachute has been deployed. The sky crane is operating.’ It was just unbelievable.

Johnson: So tell me a little bit about where Curiosity landed? Why did you choose this particular spot? And did the lander hit its mark?

Blake: Well, we think it did. We don’t know exactly where it landed but its certain it landed within the ellipse. Gale Crater is one of the oldest and deepest craters on Mars and we know that very early on Mars’ time it filled to the brim with sediment and that sediment solidified to make a rock and then later on a lot of that sediment was eroded out by wind and we are left with this big mountain in the middle called, we call it Mount Sharp. And Mount Sharp is 5,000 meters of stratify sediment and the geologist can basically read this like a book, so we are going to start from the bottom and work our way up and this will tell us a lot about the conditions of very early Mars.

Johnson: It sounds like, to put this in some perspective, it’s almost like landing this device at the bottom of the Grand Canyon. Is what it sounds like.

Blake: Yeah, it is very similar, similar distance down, actually greater distance of strata. And so the rover planners have actually figured out, they figured this out from pictures long ago, long ago being months, where we are going to go if we land where we say we did and going up in a canyon and to the left and to the right So they have the plans of where to go already done.

Johnson: Here in the Bay Area it sounds like scientists worked on one aspect of the lander, in particular called CheMin. Describe what CheMin is and how it works?

Blake: Well CheMin is one of two laboratory quality instruments that’s inside the body of the rover, and what CheMin does is it determines the mineralogy of all the sediments, or the drilled rock, that is delivered to it by the arm of the rover. And the interesting thing about minerals is that, if you know the minerals that are present in a rock, you can say what the environment was in which the rock formed. And so, what CheMin will do is it will tell you the conditions of formation of these rocks that are 3.5 – 4 billion years old in Gale Crater on Mount Sharp.

Johnson: And that would also include if there was once water there, right?

Blake: Well, that’s exactly right. We know from orbital assets that like the CRISM instrument on Mars’ reconnaissance orbiter that there are hydrated minerals, such as clays and hydrated sulfates, that are present where we are. And these hydrated minerals, we will be able to tell them with CheMin very easily. And these hydrated minerals tell us that there very likely was a habitable environment – that is, an environment where life could have begun or could have persisted over time very early in Mars history.

Johnson: Let’s finish with the two big questions, how soon do we see results and how soon do we send people to Mars?

Blake: We are going to get pictures back really continuously starting last night and certainly today. My instrument would not really deliver a result for probably three weeks to a month, and the reason being is that engineers are testing everything out, and we are kind of in the last of a first time use series. So by the time everything is checked out and the arm and the drill, then they will deliver a sample to us.

Johnson: And in terms of sending people to Mars? That’s a long ways off I imagine.

Blake: That’s kind of at the end of the chart. We are a step along the way. That’s just a huge challenge even compared to this, which was, to me, other worldly.

Johnson: Well it’s incredible that you got this far. Congratulations, David Blake is senior scientist at NASA AMES, in Moffett Field. Thank you for talking with us, and again, congratulations.

Blake: Well thank you. It was very enjoyable.

Watch QUEST TV's "Searching for Life on Mars"

More Pictures of Curiosity Lander and Landing Site

 

Curiosity will land near the foot of Mt. Sharp, inside Gale Crater. Over its two-year mission, Curiosity will explore the crater and mountain to investigate whether this area of Mars has ever offered conditions favorable for life.

About the size of a small SUV, NASA's Curiosity rover has six-wheel drive and the ability to turn in place a full 360 degrees, as well as the agility to climb steep hills.

Curiosity is equipped with 17 cameras, and the capability to send high-definition images of the Martian surface back to Earth.

Tags: astrobiology, CheMin, curiosity, David Blake, lander, mars, nasa
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