Photo by Virginia Smith

An Expert Opinion: Sandra Postel

Sandra Postel has been a leading authority on global freshwater issues for 25 years. Through her organization, The Global Water Policy Project, Postel conducts research, writes, and travels the world providing insights into water challenges and solutions. A former Pew Scholar in Conservation and the Environment, she is currently the National Geographic Society’s Freshwater Fellow —and she NEVER drinks bottled water if she can help it.

You’ve said in the future the human story will become a water story, what do you mean by that?

Water is going to be a central driver of the human experience over the next several decades and beyond. It’s about the scarcity of water; the fact that we’re running into limits in so many places around the world when it comes to water to grow food, water to keep cities expanding, and water to keep our populations supplied with what they need.

It’s been said “What oil was to the twentieth century, water will be to the twenty-first,” meaning conflict will erupt over water access.  Are wars over water inevitable?

I think water’s a more serious issue than the oil issue, given that there’s no substitute for water.  We can’t transition away from water, the way we can from oil to other sources of energy.  The idea that there will be wars over water the way there have been wars over oil; I think that’s a distraction.  There’s going to be enormous social unrest and many humanitarian crises around water and related food shortages within countries. We need to think about and plan more for these circumstances than worrying about armies mobilizing over water.  When you look at the river basins around the world, there’s more of a tendency to cooperate than to enter into conflict, so that’s a good thing.

I remember once watching David Letterman do a monologue when New York was in drought where he said, “I keep hearing about this water shortage so last night I turned on my shower and this morning it was still going strong.” How can you communicate about water scarcity when, in the first world, it’s pretty much available on demand? 

I think most people do only think about water from the point of turning on their tap.  But it’s hiding in so many other places in our lives; embedded in everything we wear, everything we eat, everything we do.  It takes about 2000 gallons a day to sustain the average American’s lifestyle.  More than half is our diet.  So helping people think about how their dietary choices increase or decrease their personal water footprint makes a difference.  Also, it takes 700 gallons to make a cotton shirt. That awareness is really missing.

According to the NRDC, it takes anywhere from 700 to 2,000 gallons of water to produce about a pound of conventional cotton; just enough to make a single t-shirt.

What have been some success stories in water conservation?

In terms of urban conservation, I think Boston is one of the best, in part because it’s in a part of the country that you don’t think of as needing to conserve so much. In the late 1980s, Boston was looking at a potential diversion of the Connecticut River to add supply to their reservoir.

The Connecticut River in western Massachussetts

But the citizens said they wanted to protect the river and its salmon populations, so they asked the water authority to take a serious look at conservation measures.  They did, and what they put in place was one of the most progressive and comprehensive conservation programs that I’ve seen.  It involved retrofitting homes, strategic pricing, education, audits of industries, fixing leaks.  A lot of older cities have tremendous leakage in the system.

Boston’s water use today is back to where it was fifty years ago.   It’s gone down 43% from the peak.  And this is greater Boston: two and a half, three million people.  The conservation program cost half as much as the alternative would have cost, and it is better for the environment. The river wasn’t diverted, and now there’s actually extra water, in a sense, surplus water in the reservoir.

Do you drink eight cups of water daily? What kind of water bottle do you use?

Photo credit: Cheryl Zook/National Geographic

I drink tap water and I drink it out of a glass –or I have any number of stainless steel bottles that I put water in if I’m going to take a hike, or play tennis, or do something outdoors.  I don’t drink bottled water unless I absolutely have to because I’m somewhere where there’s no other water available.

You grew up on Long Island, but now live in New Mexico.  Does living in an arid environment change your relationship with water?

Sure. All I have to do is look out my window to see the importance of water in our lives.  Understanding the impacts of climate change, particularly on the southwestern U.S., and what it’s going to take to sustain agriculture and populations in the West – it’s all right here.

If you want to get an idea of your own water use, try out the Water Footprint Calculator Sandra Postel helped develop with the National Geographic Society. 

We are getting very close to being able to bring back these gorgeous trees that used to dominate forests in the Eastern U.S. Now the big question is whether we should. Image courtesy of Wikimedia commons.

Around the turn of the 20th century, the forests in the eastern U.S. were dominated by the American chestnut. These “sequoia of the east” ruled the roost back then and were the cornerstone tree species. By midcentury, though, almost all of these majestic trees had been turned into shrubs.

No, this wasn’t magic. Instead, a fungus arrived from Asia that prevented the trees from growing bigger than this. Nowadays the only tall chestnuts are a few that happened to be planted outside of the tree’s old range. And even some of these are starting to be done in.

Ever since the blight started stunting the chestnut, scientists have been looking for ways to help these trees fight back. And now they may finally be getting close to a solution. Well, actually, multiple solutions.

The one I want to focus on here is a very clever genetic modification that involves moving a wheat gene into the American chestnut. Early studies look to be very promising and these trees have even been shown to be resistant in the field. The researchers are hoping to get approval soon from the U.S. government for widespread planting.

These orange spots will eventually do this tree in just like it has with most every other American chestnut. Image courtesy of Wikimedia commons.

The idea behind this method rests on the knowledge that the chestnut blight needs an acidic environment to do its dirty work. The way this little monster accomplishes this is by making and then pumping oxalic acid into the tree. This is incredibly damaging to the chestnut.

The obvious solution is to find a way to neutralize this oxalic acid. We are looking for a solution as simple as those old chemistry experiments where we neutralized hydrochloric acid with sodium hydroxide. This is where wheat can help.

Wheat makes an enzyme called oxalate oxidase (OxO) that breaks down oxalic acid. The researchers took the gene that has the instructions for this enzyme, the oxo gene, and put it into the chestnut tree. The tree now makes the enzyme so that it can neutralize the blight’s oxalic acid. This approach appears to be working in making the trees more blight-resistant.

When researchers looked at different trees that made different amounts of the enzyme, they found that only those that made a lot were resistant to the blight. In other words, there was a correlation between the amount of enzyme and resistance. When the gene was in the right place in the tree’s DNA, it could make a lot of enzyme so the tree could fight off the blight.

Just because we might be able to turn back time to when these trees ruled, should we? Image courtesy of Wikimedia commons.

So now we have a GM tree that might restore these forests back to what they were a century or so ago. Now we have to decide whether to plant them or not.

This is not really an issue of the tree having been created through genetic engineering. It is very hard to come up with plausible ways that a tree with this gene could have a significant effect on the environment. The trees aren’t modified so they make their own pesticides, survive spraying by herbicides or anything like that. They simply make an enzyme from wheat that successfully battles a killer fungus by neutralizing an acid.

No, it has more to do with upsetting the new balance that has arisen over the last few decades in the forests back east. The forests have adjusted to the loss of the American chestnut and reintroducing the tree will only plunge the forests back into a period of readjustment. This temporary state of flux will be disruptive and so should be done for more than nostalgic reasons. There should be some environmental or economic benefit in bringing the American chestnut back.

Again, this discussion is not dependent on the fact that the tree is GM. The same arguments can be made for the American/Japanese/Chinese hybrids that look to be resistant too. In fact, this discussion isn’t really that different from those brought up with regards to bringing back extinct species. Like those folks in Monty Python’s The Holy Grail, the American chestnut isn’t quite dead yet, but it is close.

So we finally have ways to bring back the American chestnut. But it may be that it took us so long to find them that we don’t need them anymore. The forests have moved on, maybe we should too.

Natural range of the American chestnut as reported in 1914. The cross hatching shows the extent of the blight back then. Image courtesy of Wikimedia commons.

How Do Scientists Think?

Field Notes:  Clancy Wolf, IslandWood    

What do you think of when you think of “science?” Do you get all nervous and think about chemistry class and trying to get the right answers on the labs?

Forget the word “science” for a minute, and go back in your memory. Can you remember a time when, say as a young child, you played in a field, beach or barn?  Maybe you spent a whole day figuring out how to skip a rock across a lake. Or what exactly you had to do to stay balanced on your two-wheeled bicycle. Those memories are what “science” is all about – asking questions, and working out ways to answer them.

As far as “The Scientific Method” goes, I’ll borrow a line from Pirates of the Caribbean: “They’re more like guidelines.” It turns out that when researchers take a look at what professionals in science really do, they do several things – but not in any specific sequence. Scientists

• Ask questions,
• Develop and use models,
• Plan and carry out investigations,
• Analyze and interpret data,
• Use mathematics and computational thinking,
• Construct explanations,
• Engage in argument from evidence, and
• Obtain, evaluate, and communicate information.

But – and this is where the inner pirate comes out – they jump around among these practices, and even ignore some at times.

Scientific Thinking and the New Standards

As a result of this new understanding of how scientists work, a better understanding of how students learn, and major advancements in our collective scientific knowledge — we are being forced to rethink how we do science education.

Over a two year period, twenty six states worked together with a 41-member writing team and other partners to develop a set of “standards” – the science practices and content that all K-12 students should master in order to be fully prepared for college, careers and citizenship. These Next Generation Science Standards were published just this April. (Note: The last major effort to define science education standards was in 1996 when the National Research Council developed the National Science Education Standards (NSES) which have influenced science education in many states.)

I find a notable part of these new standards to be the inclusion of elements of engineering. I find this exciting because it helps us think about the need to take action and work to solve problems. It’s the practical side of why we want to know stuff. It’s how we “practice” our scientific understanding.

A few years ago, Washington State’s Office of the Superintendent of Public Instruction adopted Environmental and Sustainability Learning Standards describing what all students in our public schools should know and be able to do to be environmentally and sustainability literate. These standards complement the Next Generation Science Standards in that they require understanding not only key ideas and concepts, but also the behaviors – “practices” – we all need to live responsibly within our society.

Education for Sustainability

So how do we help our children (and ourselves) learn to think scientifically and practice sustainability? One part is to make sure school districts, schools, and teachers have the necessary resources to support integrated environmental and sustainability education learning opportunities for each student. That includes opportunities for teachers to learn about the issues as well as explore how others have created learning experiences for children around these issues.

At IslandWood, an outdoor residential learning center on Bainbridge Island where I work, we run the Sustainability Education Summer Institute (SESI) every July. Our goal for the SESI Conference is that educators will gain the skills and knowledge they need to effectively provide students with experiences both in and out of school that lead to science and sustainability literacy. This year, teachers will be learning about and exploring issues around our State’s Learning Standards, gaining more insight on Science, Technology, Engineering and Math (STEM) education, and how we can work on STEM goals and Sustainability goals at the same time. (Know a teacher who might be interested attending the institute July 29-31, 2013? Send them to http://sesi.islandwood.org )

This is hard, complex stuff, though. Those we charge with helping shape future citizens – our teachers – need to have strategies to help our learners develop ways of understanding the concepts and taking action on them. The admirable goal of living sustainably (and teaching others to live sustainably) requires plenty of thinking on an ongoing basis; whether it’s thinking like a pirate– or a scientist.

Additional Links

• Next Generation Science Standards
• National Science Education Standards
• One example of how scientists really work, i.e., why there is no “Scientific Method.”
• IslandWood’s SESI website

An Expert Opinion: Frances Seymour

The former Director General at the Center for International Forestry Research, Frances Seymour has been a world leader in the effort to understand and address the impacts of tropical deforestation for 20 years. Or as she puts it, since Ben and Jerry’s released their Rainforest Crunch ice cream.

What got you interested in forests in the first place?

Growing up in Chapel Hill, [North Carolina] I was always interested in nature and I tried to think of careers that could enable me to indulge that hobby. So when I was at UNC, I majored in zoology and thought about being a wildlife veterinarian as a way to be outside. I was in graduate school at the time when tropical forests were just exploding onto the international consciousness. This was back in the era of Rainforest Crunch and the lead-up to the first Rio Earth Summit in 1992, when everybody was concerned about tropical biodiversity and indigenous peoples. So I ended up being caught up in all that and making a career out of it.

What are some of the human and ecological costs of deforestation?

When forests are lost, that means the loss of a lot of things that local communities depend on. At the local level this includes access to timber and non-timber forest products. At the landscape level forests provide various ecosystem services, like keeping clean waters in streams year-round and regulating rainfall patterns. Last but not least are the global-level human impacts. It’s estimated that greenhouse gas emissions from tropical deforestation and other land-use changes are a greater source of [C02] release than all of the planes, trains, automobiles emissions combined.

What poses the biggest risk to our forests: chopsticks, toothpicks, or toilet paper?

I would say “none of the above,” because some of the fastest and most damaging deforestation taking place right now is caused by the palm oil industry. So maybe the answer would be “your doughnuts.”

Palm oil is one of those commodities that is mostly used as an edible oil. In Asia, it’s the most commonly used oil for frying things. But in our supermarkets, it’s in, like, half the products, ranging from shampoo to peanut butter to doughnuts. And so that’s probably the greatest threat to tropical forests right now.

Is palm oil a relatively new commodity, at least on this scale?

Palm oil has been produced on an industrial scale in Indonesia and Malaysia for a long time, but the price of it has rapidly escalated. The prospect of new markets for palm oil-based biodiesel have also come on the horizon and so the incentives to invest in palm plantations have increased in recent years.

Photo by Ryan Woo/CIFOR

Photo by Daniel Murdiyarso/CIFOR

Palm oil production is responsible for significant deforestation in both of those places and, most recently, it’s begun to expand to other regions. It feels like almost every day I read a news release about another deal being done for tens or hundreds of thousands of hectares in Central Africa to be converted to an oil palm plantation. And the particular concern in a place like Indonesia is that a lot of this palm oil is being planted on peatland swamp forests. These peat swamps can be standing on layers of organic matter that has accumulated over thousands of years. They can be more than 30 feet deep.

Thirty feet deep. That’s incredible.

Think about that for a minute. When you drain and burn a peatland forest in order to plant palm oil or pulp and paper—not only do you have the pulse of emissions from the initial burning of the surface vegetation going into the atmosphere, but that organic matter that was locked up underground is suddenly liberated, releasing greenhouse gases into the air as it oxidizes and decomposes. And so the amount of carbon per hectare released into the atmosphere is many, many, many times greater than an equivalent hectare of forest not on peat swamp soils.

What’s the best way to balance sustaining the health of a forest and giving forest-dependent communities control of their resources?

I guess I would challenge the premise of the question in the following way: one of the great misconceptions about tropical deforestation is that it’s the local people who are responsible for deforestation. Communities don’t need to be convinced of the value of forest because they’re the ones who hunt in the forest and fish in the forest and gather rattan from the forest. They’re the ones who suffer when the logging trucks come in. So it’s kind of galling to blame deforestation on local communities when, in fact, the people who are profiting from deforestation tend to be elites from capital cities.

I love that you challenged me on that.

You can tell I’m not shy.

Agriculture, specifically livestock grazing, contributes to deforestation. Are you a vegetarian?

[LAUGHS] No, I’m not. Yes, it is true overall that agricultural expansion is one of the key drivers of deforestation around the world. In terms of the cattle production in the Amazon, there’s been a big effort recently to try to shift beef production to deforestation-free methods.

People that are reading this might want to know what they can do to prevent deforestation. Should they buy forest-certified lumber? Eat local meat? Eat fewer doughnuts?

With specific reference to tropical deforestation, I think there are two things: One is to be a constituency for active U.S. engagement. And then, as individual consumers, yes, it does make a difference. Buy sustainably produced FSC-certified wood products. And hopefully, over time, we’ll have credible certification systems for some of these other commodities that can be certified deforestation-free.

Did you read The Giving Tree as a kid?

Did not.

If trees could talk, what would they say to the humans right now on this planet?
Trees have a self-interest in controlling climate change. So in addition to, “Don’t cut me down,” trees would also say, “Please protect the climate,” because forests are also vulnerable to climate change. With a changing climate, forests are experiencing drought and new invasions of pests that we have haven’t seen before. And so they would be saying, “If you want to keep forests around, you need to protect the climate.” So it’s sort of the opposite of what we’ve been talking about, “If you want to protect the climate, protect forests,” but it works the other way too.

*This interview has been condensed and edited.

If your town were suddenly struck by an earthquake or hurricane, you could count on the arrival of police, firefighters, and medical technicians to aid in the emergency response. As of this past January, the US government has added a new team of responders to this list—scientists.

The Strategic Sciences Group was formed under Secretary of the Interior Ken Salazar in order to help the department “act quickly, decisively and effectively when hurricanes, droughts, oil spills, wildfires or other crises strike.” The group was initially tested as a pilot program during the Deepwater Horizon oil spill and is now a permanent part of the Department of the Interior.

But don’t expect to see people in lab coats rushing into burning buildings or diving into flooding rivers.

“The Strategic Sciences Group’s mission,” says group co-leader Gary Machlis, “is to very quickly assemble a team of scientists to develop scenarios of what the cascading consequences of a crisis might be.” These scenarios are projections of all the different ways in which the disaster might play out. The projections are then delivered to the President and other national leaders to help inform real-time, emergency-response decisions.

During Deepwater Horizon, for example, calculations regarding oil flow rates helped decision-makers respond to obvious problems such as ecosystem contamination, as well as some subtler consequences: long-term displacement of oyster harvesters, disproportionate economic impacts upon cultural communities, and diminished hurricane resilience due to wetland stress.

Deepwater Horizon in flames, April 21, 2010.
(AP Photo/U.S. Coast Guard)

With such a breadth of potential consequences to examine, its clear that the Strategic Sciences Group’s task is not simple. What is surprising however, is that many of the group’s difficulties stem from the nature of the scientific process itself.

“Scientists are very accustomed to being deliberate in their work,” says Marcia Mcnutt, who worked with the Strategic Sciences Group during her tenure as director of the United States Geological Survey. “The idea that they might get critical info on a Monday night and need to have their best guess of what that info means by six am Tuesday morning is just not the normal way science operates.”

And, Machlis adds, the rapidly determined results must also be communicated persuasively.

“It isn’t enough to do good science. You might have an extraordinary, complex scenario figured out that’s important for leaders to know, but if you can’t tell that story clearly and effectively, it’s of less value.”

These requirements—the ability to work with urgency, cope with uncertainty, and communicate well with non-scientists—separate crisis science from traditional scientific research.

When creating the Strategic Sciences Group, Machlis responded to these unique demands by borrowing ideas from an unusual agency: The Office of Strategic Services, or OSS, which was established during World War II to coordinate espionage activities behind enemy lines.

Machlis says he has learned four important lessons from the historic military-intelligence organization:

OSS founder Maj. Gen. William J. Donovan with members of the OSS
Photo Courtesy of the OSS Society

“The ideal candidate for the OSS were PhD’s that could win a bar fight,” says Machlis.

While martial arts training is not an actual requirement, the Strategic Sciences Group does seek scientists with a certain mental and physical tenacity. “They‘ve got to be expert in their own discipline, able to transcend their own discipline and work well with other scientists, and they have to be able to work extremely hard under very intense conditions.”

“Our goal is to get the very best people in the field working on these science teams. It is less about do we need one person from this agency and one person from this agency to make sure it’s representative.”

From government scientists to graduate students, anyone with the necessary skills can be recruited and put onto Machlis’ lists, or “rosters”.

US Department of the Interior Strategic Sciences Working Group, New Orleans, LA, July 2010. Photo Credit: Jason Newman

Machlis ensures that the rosters are highly interdisciplinary. The 30 scientists who have already been called to action include “an anthropologist with expertise in disaster response from Louisiana, a public health medical officer from Washington, DC, a coastal geomorphologist from California, an ecologist working with a major natural history museum, and a Forest Service social scientist with expertise in urban ecology.”

Such diversity allows the Strategic Sciences Group to be highly adaptable.

“Each crisis that might happen, whether it’s an oil spill, whether it’s an earth quake, whether it’s a dam failure, there’s always going to be many elements of it that are unique. We need to be flexible enough to choose a team that has reliable expert scientists appropriate to that crisis.”

“We stay focused on the mission rather than developing a lot of complicated, time-consuming bureaucratic processes.”

In order to avoid creating a large government agency, Machlis only activates the rostered scientists when a disaster occurs. At all other times, the Strategic Sciences Group is made up of only three people.

This three person team, when there are no current crises, spends its time evaluating the consequences of potential crises.

By considering situations such as “a forest fire in the sierras during Yosemite’s tourist season, or a pandemic, or an arctic oil spill,” the group hopes to pre-emptively increase response preparedness. Ultimately, Machlis aims to have the capacity to address simultaneous, bi-coastal disasters. For example: an earthquake in California and a hurricane in New York on the same day.

When will the group be ready for such a situation?

“I would hope that we’re prepared for that within the year.”

Mark that down as December 31st, 2013–the date when you can expect not only police and firefighters, but also scientists, to play a role in addressing the next major natural or man-made disaster.

Are the benefits of genetically engineered foods worth the risks?

Next Meal: Engineering Food explores how genetically engineered crops are made, their pros and cons, and what the future holds for research and regulations such as labeling.
 

Ever wondered what genetically engineered crops and other foods are in the pipeline?

Click through the map below and find out what's in your next meal… or in the forest on your next camping trip.

For a bigger version of this map, click on the link below.

View Genetically Engineered Foods in the Pipeline in a larger map

Conventional plant breeding vs. genetic engineering – 5 differences:

1. When did we start using each technique?

 
Plant breeding is some 10,000 years old – as old as agriculture itself.

“The ancestors of tomatoes were the size of my thumb and they tasted very bad,” said Eduardo Blumwald, plant biologist at the University of California at Davis. “And breeding gave us what we have right now.”

In the mid-1990s, tomatoes genetically engineered in California were made into a tomato paste that sold well in England. But the tomatoes were short-lived. Photo: Alan McHughen.

The first genetically engineered food to be commercialized, the Flavr Savr tomato, was sold by Calgene, a Davis company, starting in 1994. The tomato was engineered to stay firm on the vine for longer, but it was short-lived.

Monsanto, the Missouri-based seed company, started selling genetically engineered soybeans and cotton in 1996. The soybeans tolerate the herbicide Roundup, so that farmers can spray it on weeds without hurting their crop in the process. The cotton keeps away pests like the bollworm.
 

2. How do these two techniques work?

“Classical plant breeding involves taking the female eggs from one plant and bringing them together with the male parts of another plant,” said Peggy Lemaux, plant biologist at the University of California at Berkeley. “And then all that genetic information gets mixed up. Half of the information in the progeny – or children – of that cross comes from the mother and half comes from the father. And it just all gets mixed up.”

Depending on the plant, breeders use different strategies to cross them. Corn breeders, for example, gather pollen from female plants and shake it onto male plants. Plants such as cucumbers usually contain both female and male flowers on each plant. Breeders remove the male part from one flower and attach it to a female flower.

Plant biologist Peggy Lemaux, at the University of California-Berkeley, uses a "gene gun" to genetically engineer crops like corn.

In contrast with breeding, genetic engineering involves only one or a few genes.

“With genetic engineering, it’s just moving very small parts of the genetic information. You might take it out of one plant and move it into another plant,” said Lemaux.

In genetic engineering, genes can be transported into a plant by a type of soil bacterium. Or they can be injected into a plant using a tool called a gene gun.
 

3. What can you do with each one?

Classical plant breeding allows scientists to do things like breed disease resistance or a higher-protein content into crops like wheat, said Jorge Dubcovsky, leader of the wheat breeding program at the University of California at Davis.

But when they’re breeding, scientists have to cross plants that are closely related to each other.

“Classical breeding is done between closely related plants, so you might take a wild variety of rice, for example, and you could cross that with modern cultivated rice,” said Peggy Lemaux. “However, maybe there are traits that you want, that you can’t find in a wild variety of rice. Maybe you want to introduce some vitamin or mineral, and you can’t find a wild rice species that would give you that particular trait. So what you have to do is you have to go and find some other organism that does make, let’s say, vitamin A, and you can pull that information out from that plant and put it in.”

In that scenario, genetic engineering would be required. Engineering would also be required to tweak a gene in such a way that it produces more or less of a desired trait.
 

4. Is conventional plant breeding low-tech, while genetic engineering is high-tech?

Genetic engineering can be more expensive than conventional plant breeding, and is usually faster. But this doesn’t mean that breeding is as low-tech as you might think. In the past 15 years or so, plant breeders have been able to speed up the crossing process by using genetic markers.

“The markers allow me to see the genes that I have bred into a plant,” said Jorge Dubcovsky.

Many genes that scientists set out to breed into plants are difficult to see and expensive to find within the plant. A genetic marker is a piece of DNA that is easy to see and inexpensive to find within a plant. So scientists identify the markers that are on either side of the gene they’re trying to breed into a plant. This way, when they have crossed their plants to contain that gene, they can easily and inexpensively find out which plants contain their gene of interest by looking for the markers, rather than for the gene. Markers are like tiny flags on either side of the gene that make it visible to researchers.
 

5. Do scientists do either one or the other?

Usually, some researchers specialize in plant breeding and others in genetic engineering. But both types of scientists work closely to improve crops, said Eduardo Blumwald, who is genetically engineering rice to be drought-tolerant.

“We are placing new genes in those varieties which plant breeders have bred,” said Blumwald.

Photo by Rachael Rufino

While most people are out enjoying the warmer weather spring offers, there are some who cannot wait to make their way underground. With the rainy season behind us, California Caverns are opening up for those who aren't afraid of the dark.

Tour guides interpret the eerie speleothems (cave formations), created by water droplets and mineral deposits. Most of the formations follow the laws of gravity. Stalactites appear to grow downward as water droplets following down the same path leave minerals behind. Stalagmites on the other hand, appear to grow upward, as water droplets fall and land in the same place depositing minerals over time. Helictite crystals, however, actually defy gravity. Although their formation is not fully understood, water pressure and capillary forces are said to play a key role. This results in one of the most delicate, extraterrestrial-looking speleothems.

Photo by Rachael Rufino

Simpler formation names inspired by more familiar objects include "soda straws," "angel wings," and "bacon." Their formation is so slow, a speleothem that is a couple inches long can be several hundred years old.

Photo by Rachael Rufino

Although bats are an iconic cave inhabitant, you won't find them here. Small crustaceans are one of the few residents confirmed living in this isolated environment. One species is endemic to Black Chasm Cavern, meaning, the entire population exists only in that cave.

An environment that is so secluded means that the slightest disturbance can throw its ecosystem off balance. Algae has unnaturally began to grow in the caves because of the heat given off by light bulbs. When touring, it is important to observe the formations without touching them, as the oils from our skin can degrade the fragile speleothems. To help preserve these chambers, tour guides will immediately turn lights off when leaving, and in California Cavern, a pristine chamber called the "Jungle Room" is only shown to visitors who have demonstrated respect for the cave and its rules.

Photo by Rachael Rufino

Located just 3 hours from San Francisco, exploring Black Chasm Cavern, California Cavern and Moaning Cavern is a fascinating way to spend the weekend for all ages.

I don't have time for this, I need to get back to writing grants! Image courtesy of David Shankbone, Wikimedia Commons.

If you’re a scientist these days, getting the money to do your research is a lot like getting into Stanford or Yale. Assuming you aren’t rich or connected, being incredibly skilled, hardworking and accomplished isn’t enough. You need to get lucky too.

The big difference is that in terms of funding for research, there aren’t really any back up schools. If you don’t get into your Ivy League college, you don’t get your college degree. The best you can do is scrape together a few part-time jobs to stay in business so you can apply over and over again to the same school. No wonder so many scientists are becoming discouraged.

For those of you who don’t know how scientists at universities get their money, here is a quick, crash course. First off, scientists aren’t paid by a university to do their research. They are expected to raise that money on their own. They are given a bit of money to get started, but the university supplies almost no money after that. In fact, they take a good chunk of the money you manage to raise for overhead costs (buildings, electricity, name recognition, etc.).

This didn’t used to be a big deal. Yes, it was an inconvenience but there was enough money so that if you had a good idea and some data to support it, you had a pretty good shot at getting funded. This is no longer true.

These days most higher-level scientists are spending less and less time doing science and more and more time writing grants to try to get research funded. If they don’t have a big name and/or come from a big school, odds are most if not all of the grants won’t be funded. And even if they have the reputation and come from what is deemed to be a big school, they still may end up penniless.

Someone I know at Stanford summarized his situation like this:

This year I'll be submitting six RO1 grants, each of which take about a month's worth of effort. Given that the current funding levels are less than 10%, I'll be lucky if one gets funded so I can keep doing my research. Three of these proposals are seeking funding to continue existing research projects that serve the scientific community; if they aren’t funded, those projects will stop.

As you can tell, he is writing as fast as he can to try to keep at least some of his projects going. He is not doing much research on his own, he is just trying to get enough money so the graduate students and other people in his lab can do some science. Not what he was trained for!

Not only that, but as he says, some of his ongoing projects will lose their funding. This isn’t because they aren’t worthy. Instead they won’t be funded because they didn’t get the lucky six numbers to win the lottery this round.

President Obama recognizes the problems with science funding.

Chaotic funding like this slows research down as ideas are not allowed to flower but instead die or go dormant. And even if they are picked up again, research is slowed as the new group has to learn the subtleties of that particular project. This is no way to run a business!

At least some people in government are recognizing this reality. President Obama in a speech to the National Academy of Sciences suggested that sequestration could cost two years of research. And this is just the sequestration; it doesn’t include the lost years from the drop off in funding that has already happened in the last few years.

As you might expect, this isn’t just a U.S. problem. A recent article in the Guardian points out that the same sorts of things are happening in Europe and Australia too.

In a time of decreased funding, we have to decide if having fewer scientists able to do research is OK. If it is, then we can keep the same system in place and have scientists writing grant after grant, trying to raise money for their research. Hopefully the best grant writers are also the best scientists.

If we want more scientists able to do research, then we have to decide what to do. One idea might be to streamline the granting process to save money so that more grants are funded. The occasional stinker of a project might slip through, but that might be OK if many more grants can be funded. Another idea would be more money for research, but you can’t squeeze blood from a turnip. There simply may not be the money to fund research under the current system so that a scientist has a reasonable chance at getting funded.

The worst part is we have to count on Congress to try to deal with this. I suspect things will go on like they have been for a very long time.

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.

H. pylori has lived in our stomachs for 200,000 years. (Photo: Dr. Yutaka Tsutsumi)

Helicobacter pylori

Humans have a love-hate relationship with H. pylori. It has dwelled inside our stomachs for 200,000 or so years, but its role is unclear. Scientists believe the microbe causes peptic ulcers and have linked it with an increased risk of stomach cancer. But the percentage of people with H. pylori has been shrinking, particularly in the Western world where antibiotic use has been widespread for more than half a century. Those lacking in H. pylori may be at higher risk for asthma or obesity, since the bacteria helps tell us when we’re full. Scientists aren’t sure whether the absence of the microbe actually causes asthma or obesity, but the two occurrences do correlate.

Source

C. difficile can cause some nasty problems if left unchecked by "good" bacteria. (Photo: Centers for Disease Control)

The “good” bacteria in your gut often keep bad stuff at bay. When the good guys are destroyed (possibly with antibiotics), C. difficile takes over, which can cause severe diarrhea or deadly inflammation of the colon. The condition most commonly affects hospitalized older adults or those in long-term care. The cure: more antibiotics — or a fecal transplant.

Source

Bifidobacterium

Bifidobacterium lives throughout the body and can be damaged by antibiotic treatments. (Photo: Wikimedia Commons)

The gut biota ecosystem is a dramatically changing environment in the first two years of life. Bifidobacterium include a range of bacteria species that exist symbiotically throughout our bodies. But the evolution of Bifidobacterium in infant bodies can be stunted by early antibiotic treatment. The bacteria are linked with many probiotic benefits, and scientists do not yet understand the long-term health consequences of reducing their numbers.

Source

P. gingivalis can make your teeth fall out. (Photo: Flickr user AJC1)

Porphyromonas gingivalis

Did you brush your teeth this morning? The microflora in our mouths can cause some real problems. Take P. gingivalis (pictured). The bacteria places a role in the onset of periodontitis, an inflammation of the gums that causes teeth to fall out. P. gingivalis is also associated with rheumatoid arthritis and heart disease. It’s less abundant in the mouth than, say, Streptococcus parasanguinis. Those bacteria colonize the surface of your teeth, forming plaque.

Lighter than an SUV and covered with more than 12,000 solar cells, Solar Impulse, the world's first solar plane that can fly day and night without recharging, launched from Moffett Field this morning in a cross country voyage. The $150million project initiated by co-pilots Bertrand Piccard and André Borschberg will test the limits of solar aviation and be a proving ground for a planned trip across the world in 2015.

At 5:15am, a crowd of 25 journalists gathered around Piccard as he answered questions about what it's like to fly the plane and whether he was exhausted. "I'll be in the air for 20 hours but I've been dreaming of this flight for 10 years so there is no time to be tired," he said. Researchers from the NASA Ames Research Center also stood 50 feet from the tarmac to catch a glimpse of the plane taking off.

The single-seater plane was financed by several large corporations including Omega, Solvay and Deutsche Bank. The companies developed new technologies in order to create the aircraft. The monocrystalline solar cells needed to be flexible enough to curve atop the wings and the resulting cells are the thickness of a human hair.

Solar cells power four electric engines and excess energy is stored in four lithium batteries located below the wings. Since the batteries account for 25 percent of the plane's total weigh other elements had to be eliminated. There is no heating or cooling system and many metal parts were replaced with plastic; Solvay designed ultra-light polymers that could replace metal in the instrument panels and control box.

For all of the plane's high-tech innovation it's far from ready for commercialization. Flying at 43 miles per hour, it could easily be outpaced by a pigeon. But Piccard has said the goal is not speed but duration and Borschberg believes the technology developed for this plane could be used by everyone. "All the technology we have  used in the airplane can be used on the ground, it wasn't developed by aviation companies," Borschberg said. "One day it could be used in refrigerators in your home or in electric batteries in your car."

The plane will fly at 28,000 feet, stopping in Phoenix, Dallas and Washington D.C. before touching down in New York. The pilots will take turns flying, switching out at each city where they will talk to the public about the plane.

To watch live coverage of the flight and watch Piccard as he talks about what he sees from above visit the live stream.

Smile, universe, for your baby picture! Maps of the early universe by the COBE, WMAP, and Planck missions. Image credit: NASA

On news that the universe may be 100 million years older than previously estimated, cosmological markets have seen a reduction in the benchmark of universal expansion, the Hubble Constant, down to a new low of 67.15 kilometers per second per megaparsec. This has led to a drop in the dark energy market, down from initial estimates by 3.1% to 68.3% of the total universal mass/energy inventory. On the brighter side, stocks of the highly sought-after dark matter commodities are up to 26.8%, and good-old reliable normal matter fundamentals have inched upward to 4.9%, up from the previous 4.6%.

The news comes not from Wall Street but from cosmological observations by the European Space Agency's Planck mission, and analysis of those measurements by European, NASA and Canadian scientists.

What do the numbers mean?

That the age of the universe is 100 million years greater than previously calculated is interesting, but it won't force the Barenaked Ladies to change the lyrics in the Big Bang Theory's opening theme song; "…nearly 14 billion years ago…" works whether the number is 13.7 or the more recent 13.8 billion.

The small refinements in the percentages of the universe composed of normal matter, dark matter and dark energy are probably more interesting to scientists as far as the absolute numbers go. But the mere fact that a quarter of the universe is made of stuff we can't see (dark matter) and over two-thirds of the universe is made of stuff we can neither see nor at present understand (dark energy) is a stupefying fact. It means that what we can see in the universe (planets, stars, galaxies—normal matter) is only about 5% of what's actually there. Stupefying!

Planck's mission is to measure minute differences in the brightness of the Cosmic Microwave Background (CMB) radiation, the faint glow of microwaves coming from every direction in the sky. Originally discovered by accident in 1964, CMB radiation comes from the greatest observable distances in the universe, and from the earliest time that light became able to travel freely through space.

Astronomers became very interested in these cosmic microwave emissions, for in collecting and measuring those photons they were essentially taking a picture of the very early universe, not long after the Big Bang (the theory, not the TV show). The CMB is the "afterglow of creation," and for astronomers to discover and study it was something akin to when anthropologists first found fossils of the earliest hominids.

When you look out at distant galaxies you are seeing the light that left them in the distant past—how far in the past depends on how far away the galaxy is. The most distant galaxy that we have seen is a portal back in time over 13 billion years, a time when the universe was barely past infancy. But look a bit farther into space, a bit further backward in time, and you are looking at a time before galaxies had formed from the expanding gaseous universe.

The limit of our ability to peer backward is met at the time before which the hot gases of the Big Bang aftermath were too dense for light to travel freely, and instead bounced around within the hot dense soup (those lyrics also need no adjustment) of atomic nuclei and electrons–similar to how light bounces between water droplets in a cloud. We see this far, but no farther because we are looking into an opaque cloud that existed before the universe was 370,000 years young.

As our picture-taking of the earliest face of the universe became more refined, a more detailed map of the CMB's variations in brightness was resolved, starting with the relatively blurry blotch-map brought by the COBE mission, to a more detailed all-sky image by the WMAP mission, and now the clearest picture yet by Planck.

The color variations in the map represent minute differences in the temperature and density of the gases of the early universe—subtle variations that eventually snowballed (so to speak) to become denser concentrations of matter, and the seeds of the earliest galaxies and galaxy clusters.

So, in comparing the blotchy facial features of this infant shot to photos of the universe taken at later times we have assembled a more complete life picture of how the cosmos has grown and developed. And no one had to change the lyrics of their song either!

To make this side trip, turn off I-80 just west of Sacramento onto US 50. This point is the western end of US 50; you can stay on that historic route past South Lake Tahoe and across Nevada to reach the Atlantic at Ocean City, Maryland.

Route 50 starts at sea level and stays on the level ground of the Central Valley, following the American River toward the mountains. Twenty miles later you've climbed just 130 feet. All of the ups and downs of the road are related to interchanges and overcrossings, not topography. You won't see it from the highway, but most of the ground is gravel tailings, piled up over decades of gold mining in the bed of the American River. The river course is open to the public in Sacramento County's American River Parkway.

At Hazel Avenue, 21 miles into the drive, exit and turn left (just above the "E" in Gold River on the map). It's a few hundred yards to the Nimbus Fish Hatchery, which has been here since the 1950s. You can tour the hatchery, or you can sit and watch the river flow. The last dam on the river, the relatively low Nimbus Dam, is just to the east.

Photos by Andrew Alden

And here we finally have topography, and rocks. The rock in the cliffs is mapped as the Turlock Lake Formation, which consists of sandstone and siltstone about a half million years old. At that time the rising Sierra Nevada was shedding this sediment in vast fan-shaped aprons up and down the eastern Central Valley. The wonderful fossil beds of the Fairmead Landfill site, down by Chowchilla, are in this formation, but no one has reported anything like that around here.

Return to US 50, go east another mile, and take Folsom Boulevard north. Now let's look at the geologic map of the route (derived from the State Geologic Map).

The Turlock Lake Formation makes up most of the area marked QPc, and the pink area is granite. That's what you'll see in the northern half of this side trip, between the towns of Folsom and Loomis. But first you pass a high pile of clean boulder gravel, two miles from US 50.

This is just a tiny bit of the tailings left behind by the gold syndicates, much of it over a century ago. Pull over if you can and climb on it. Folsom began as a gold-rush town, and if you have the time there's a lot of history to explore. Along here you'll also catch glimpses of the sprawling, monumental Folsom Dam, built in the 1950s for flood control and power generation. Folsom Lake behind it is a major outdoor asset for the capital region. There are several opportunities along the route to visit the lake and wet your feet in Folsom Lake State Recreation Area.

North of Folsom, the road will take you all the way to Auburn if you like, but we'll leave it at the town of Granite Bay and take Laird Road north to I-80 at Loomis. This is the pleasant, green part of the drive. By now you've surely noticed the abundant granite boulders and outcrops. They're all part of the Rocklin Pluton.

This is the same rock that makes up the High Sierra, but here it's humble and charming instead of grand and rugged. If it were lifted up three miles and sculpted by erosion for a few million years, it would look like Yosemite. The Rocklin Pluton is an outlier, far to the west of most Sierran granitic intrusions. Its high-quality stone, so convenient to rail and river shipping, was first quarried early during statehood and has been used in public buildings and industrial infrastructure ever since. To get deeper into the subject, once back on I-80 you can take the next exit, Penryn Road, and visit the old Griffith Quarry.

The cat of many names–mountain lion, puma, cougar, catamount, panther, to name a few–speaks to the once widespread distribution of Puma concolor across the continent. The wide-ranging carnivore can adapt to nearly any landscape. It remains to be seen whether it can adapt to the expansive activities of the human being. Photo: Liza Gross

Two years ago, a stellar cast of ecologists changed the way conservation scientists think about biodiversity. As we tumble headlong into the sixth great extinction, biologists have focused largely on protecting regions with the highest number of species. By saving the most species, the thinking goes, you’ll conserve the greatest number of ecological interactions and so the greatest biodiversity. But in a study that drew on ecological theory and contemporary studies of apex predators like wolves and pumas, the all-star team of ecologists found that some species matter more than others. Losing top predators, they argued, can have far-reaching, irreversible effects on the structure, function and biodiversity of ecosystems.

Ecological theory predicts that changes in the abundance and distribution of top predators can cause substantial shifts in ecosystems. And recent studies—many published in the new millennium—have shown how theoretical predictions play out on the landscape. The collapse of sea otter populations on Amchitka Island in the Aleutian Islands decimated kelp forests by allowing unfettered expansion of sea urchins, the otters’ main food. The loss of wolves in Yellowstone’s Lamar River Valley famously allowed elk to forage with abandon, arresting the development of streamside willows and other riparian vegetation. In Venezuela, forests without jaguars, pumas and eagles had almost no vegetative underbrush compared to the lush understory in forests where predators kept ungulate herbivores in check.

But, according to the study, the loss of large top predators can also lead to soaring rates of wildfires, infectious disease and carbon emissions, and degrade water quality and nutrient cycles.

These “top down” trophic cascades, which the ecologists dubbed “trophic downgrading,” have been documented from the poles to the equators and every major biome in between, making the loss of top predators, they wrote, “arguably humankind’s most pervasive influence on the natural world." Earth has weathered five mass extinctions but never before at the hands of one species—human beings. And we humans seem hell bent on clearing the Earth of larger bodied apex predators.

I considered all this as I read a new paper from wildlife ecologist Chris Wilmer’s lab (published last week in PLOS ONE) that looks at how human development affects pumas. Like most large carnivores, pumas need vast territories to hunt, find mates and raise young. Pumas living in the San Francisco Bay Area have no such luck. Wilmers, an associate professor of environmental studies at the University of California-Santa Cruz, has been studying the effects of habitat fragmentation on the behavior, ecology and even the physiology of pumas around the Santa Cruz Mountains. He develops cutting-edge GPS collars to track both the location and behavior of his animals.

Fragmented landscapes often pave the way to extinction for wide-ranging large carnivores like pumas, with cascading effects. Freed from the threat of top predators, smaller carnivores like foxes increase in number, driving declines in birds and small mammals. But habitat fragmentation can produce effects similar to extinction because large predators tend to avoid small fragmented parcels. Given the heterogeneous patterns of human developments—with houses and other structures interspersed among natural areas—predicting how animals might respond, and with what consequences, presents a serious challenge.

Since pumas make risk-benefit calculations just like the rest of us and typically avoid humans—their biggest cause of death, aside from roads—Wilmers wanted to know what factors govern their decisions. He and his team figured the cats would steer clear of neighborhoods, where they’d risk seeing their nemesis in various activities, more than roads, where traffic can be sporadic. And they predicted the cats would respond differently depending on their reproductive status. If running into humans meant losing a meal, that would prove less costly from an evolutionary perspective, than if it meant losing a chance to mate or raise young—since, as any evolutionary biologist will tell you, we exist primarily to reproduce.

The team combined their GPS data with field visits to determine whether cats were simply going about their business—that is, feeding (based on the analysis of GPS data and confirmed by finding prey remains) or moving about the landscape (GPS readings not linked to kill or den sites)—or engaged in reproductive behavior—denning (indicated by a female staying within a spot and making repeated return visits) or communicating (indicated by “scrapes,” urine-soaked leaves and debris mounded with the hind feet, the puma version of “here’s my number”).

As predicted, the cats’ response to developments varied with their reproductive status. The data collected on their 20 collared pumas (12 females and 8 males) showed that the animals give human developments a wider berth when engaged in reproductive behaviors. Given how frequently human run-ins result in death for pumas around the Bay Area, it’s not surprising that evolutionary pressures selected against placing the next generation at risk. Similarly, the cats seem to have learned that placing their calling card near trails leaves them vulnerable to destruction by hikers and bikers.

Still, it appears that taking care of large cubs makes mom willing to take more risks. The team found that females with dependent young showed higher tolerance for residential developments than males, possibly because they can’t afford to be choosy about where they find prey. Still, one male in the study did go near developments—a young male seeking new territory—an extremely risky behavior that the sexually immature male shot in Berkeley’s Gourmet Ghetto learned too late.

There’s no doubt that our behavior influences the big cats’ behavior. If you live on the edge of puma habitat and plant lush gardens, you’ll attract deer—and likely their ancient predator. If you don’t safeguard your goats and sheep in enclosed pens at night, you’re just asking for trouble. An astonishing eight of the 11 adult pumas the team studied were shot for attacking livestock.

By understanding where, when and how pumas use their increasingly fragmented habitat, Wilmers and his team can predict how they might respond as development continues. They can also predict, and hopefully mitigate, likely conflicts between humans and the increasingly boxed-in carnivores. But ecologists, even the best ecologists, can do only so much. They need the rest of us to decide whether we’re ready to reverse the trophic downgrading of the planet before it’s too late.

Photograph courtesy of kfisto via Creative Commons licensing.

How would you like a job that involves shopping at the grocery store with the company credit card and cooking dishes like stir-fry? This describes Tosh Hotchi’s job, but he isn’t a chef. He is part of a research team that studies how to build healthy, efficient homes, including how to improve the quality of air inside a home through better ventilation. Hotchi is helping to study a major source of indoor pollutant: cooking.

When people think of air pollution, they usually picture a factory spewing a plume of toxic chemicals into the air. But indoor air pollution causes significant health effects such as respiratory illness, asthma attacks, cancer and premature death. Californians spend over 45 billion dollars each year on these health impacts, according to a study by the California Air Resources Board. This is in part because they spend about 90% of their time indoors, which is typical for people living in a developed country.

Scientists at the Lawrence Berkeley National Laboratory (Berkeley Lab) have identified which indoor air pollutants cause the greatest health consequences. In a paper published in Environmental Health Perspectives, they reported that fine particles with a diameter of 2.5 μm or less, formaldehyde and acrolein are the worst indoor contaminants for non-smoking households.

Fine particulates are found indoors mainly due to cooking, burning candles or incense, tobacco smoke and outdoor sources that leak inside. These fine particulates cause significant health problems – stroke, heart disease, chronic bronchitis and premature death.

Formaldehyde is mainly emitted by materials used in home construction and furniture, such as particle board, paneling and foam insulation. It also comes from cooking and tobacco smoke. Formaldehyde is a lung irritant that can trigger asthma attacks and it may cause cancer.

Acrolein was used as a chemical weapon in World War I. Acrolein in the home is primarily from cooking (especially oils) and tobacco smoke. It is a strong irritant for the skin, eyes and nasal passages.

“Think about what you're putting in your home,” says Melissa Lunden, a Berkeley Lab staff engineer. “Most of us have to cook, but do you need the candles, incense and air fresheners? Freshening your air requires taking stuff out, not putting more stuff in.”

Berkeley Lab scientists are now looking for ways to improve indoor air quality by developing better standards for residential buildings and new tests to measure these hazardous pollutants. For example, their Berkeley Lab report recommends to regulators that whole-residence ventilation rates should focus on controlling formaldehyde and acrolein, whereas filtration should be used to remove fine particles pollutants.

Since cooking is a major source of indoor air pollutants, Berkeley Lab scientists have also evaluated the effectiveness of cooking exhaust hoods. Their study results showed that cooking hoods should be redesigned and new rating standards are needed to help consumers know how effective a cooking hood is at removing pollutants. However, they also found that indoor air quality can be significantly improved by simply cooking on the back burners of your stove, using higher fan settings and turning the fan on before you start cooking. Further research on cooking-induced pollutants is underway using a new demonstration kitchen to study real-life cooking conditions. During these studies, Tosh Hotchi’s stir-fry and cookies are just a happy bonus for his co-workers like Melissa Lunden.

Learn more about how air quality affects your health this week during Air Quality Awareness Week.

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/2013/04/26/grappling-with-rising-tides/?utm_source=rss&utm_medium=rss&utm_campaign=grappling-with-rising-tides http://science.kqed.org/quest/2013/04/26/grappling-with-rising-tides/#comments Fri, 26 Apr 2013 15:00:30 +0000 Sharol Nelson-Embry http://science.kqed.org/quest/?p=53186

Last December, the King Tides brought high water very close to the top of a containment wall along the shore in Alameda. Photo courtesy of East Bay Regional Park District.

Strolling along the Bay Trail at Crown Memorial State Beach in Alameda a few weekends ago with a group of naturalists and college students at a professional workshop, we looked for areas that were inundated by the King Tides last winter.  We stood on trails and turf that had been underwater during those extreme high tides and discussed scientists’ predictions that high tide events, like King Tides, are likely to become the normal high tides in coming years.  As seawater warms, it will expand as well as increase due to polar ice cap melting.

"In California, we are very likely to experience a sea level rise of 16 inches by 2050 and 55 inches (1.4 meters) by 2100, and much more after that."  Sea Level Rise and the Future of the Bay Area, SPUR

The edges of our shoreline “bathtub” won’t be able to contain the overflow as the moon and sun interact and tides edge up and over into shoreline parks, roadways, homes and businesses.  You can explore the National Oceanic and Atmospheric Administration interactive model of how the rising tides may impact our coastlines. Much of my hometown, with an elevation of 30 feet above sea level, may be underwater at the predicted high water level of 55 inches above current high-high tide. My house would be above water, but I wouldn't be able to get to work due to flooded roadways. Sea level rise predictions are evolving as more information is gathered and assessed. The models continue to be refined.

The King Tide nearly cut off the trail at Crown Beach leading out to a popular fishing point. Photo courtesy of East Bay Regional Park District.

The good news about sea level rise is that these are long-term predictions, allowing us time to prepare.  As CAKE (Climate Adaptation Knowledge Exchange website) states, “Don’t Panic.”  It’s a great site to learn more about climate change basics and sea level rise science, as well as access tools available to municipalities to plan for climate change mitigation measures.

Many municipalities are working together on a regional approach.  In the East Bay this regional working group is referred to as “Adapting to Rising Tides (ART).”  It’s led by the Bay Conservation and Development Committee (BCDC) and National Oceanic and Atmospheric Administration (NOAA) Coastal Services Center with participation by two regional park agencies, East Bay Regional Park District and Hayward Area Recreation District, along with local, regional, state and federal agencies and organizations, as well as non-profit and private associations.  ART is looking at potential climate change impacts and subsequent effects to be addressed in this Climate Impacts Statement.  For more photos of King Tides around the Bay Area and California, check out the King Tides Initiative website.  What steps is your area taking to prepare for future sea level rise?

The Calaveras Reservoir dam, east of Milpitas, is a massive earthen structure built across Calaveras Creek in 1925. These traditional dam designs are generally robust—the Crystal Springs Reservoir on the Peninsula has one that easily weathered the 1906 earthquake while the fault moved beneath it. However, the Calaveras Dam needed more work. The reservoir needs to be a reliable six-month backup water supply in case the Hetch Hetchy Aqueduct is out of action. And what could damage the aqueduct? Among other things, a major earthquake on the Calaveras fault, which happens to run right under the Calaveras Reservoir next to the dam.

The plan for meeting this dire scenario was to build a new dam just downstream of the old one. It will use the existing hills on either side of the creek as buttresses and be largely made of the rock excavated from the hills. The work was proceeding without incident until June of last year when excavators on the western buttress found signs of a huge, ancient landslide in the Temblor Formation.

Cutting into the hillslope under those circumstances would risk reactivating the slide, which could endanger the workers and threaten the new dam ever afterward. So now they will cut deeper to create a shallower slope, producing about a million and a half cubic yards of extra rubble and pushing the construction schedule back three years.

Here's a view of the project as seen looking south from Sunol Regional Wilderness in July 2012. The reservoir, its water level drawn down for safety reasons, is just visible between the two cuts making up the buttresses for the new dam. The cut on the left (the right bank of Calaveras Creek) is in bluish metamorphic rock of the Franciscan Complex, and the cut on the right is in the much younger brown sandstone of the Temblor Formation. (The chopped-up hill in the middle is downstream from the dam site; the creek runs around it on the left side.)

The hill on the right, where the landslide was discovered, is Observation Hill. Both it and the smaller hill at center are composed of Temblor Formation sandstone. Photo by Andrew Alden

The landslide was discovered in the Temblor Formation. Here's the part of the Alameda County geologic map that covers the area. The photo above was taken from roughly the "25" mark at the top of the map. The solid black lines running north-south down the middle are major strands of the Calaveras fault.

From oldest to youngest: KJfm, Franciscan melange; Ks, sandstone of Cretaceous age; Ttem, Temblor Formation (Miocene age); Tcs, Claremont Shale (cousin of the Monterey Formation); To, Oursan Sandstone; Tbr, Briones Formation.

The amended dam plan, filed with the San Francisco Public Utilities Commission last December, shows an east-west cross section of the dam site. The extra digging will happen on the left side to create a slope that is less steep and more stable.

From the Addendum to Environmental Impact Report (Dec. 13, 2012), San Francisco Public Utilities Commission

I have to say a little about the Temblor Formation, which occurs mostly in the southern Central Valley beneath the Monterey Formation. It gets its name from the Temblor Range, where its type section was described. And the Temblor Range got its name after the great 1857 earthquake ripped through the area. It's a coarse-grained marine sandstone full of fossils, and this spot appears to be its northernmost outcrop—right next to another earthquake fault.

The Temblor is strong stone, but landslides can affect any kind of rock if it's fractured enough. And around major faults like the Calaveras, everything can be assumed to be fractured. The mountains of the Bay Area look beautiful and strong, but watch them for a few thousand years and you'll find them rather crumbly. Alternatively, scientists with the right equipment can survey the ground with millimeter precision. In the Bay Area's steeper hills they have detected many large, old landslides that are creeping very slowly, as they have for centuries. Maybe the landslide at the dam site was just pausing for breath. Better for the Calaveras Reservoir project to get this one out of the way.

Check out the original activity post over at Do Now for more information.

Do Now is a weekly activity for students to engage and respond to current issues using social media tools like Twitter. KQED aims to introduce 21st Century skills and add value to learning through the integration of relevant local content and new media tools and technologies. Do Now gives students a chance to practice civic engagement and digital citizenship skills while they explore ways to connect topics in their classes to the present day.

Do Now #74: Earth Day | EdspaceTo respond to the Do Now, you can comment below or tweet your response. Be sure to begin your tweet with @KQEDEdspace and end it with #KQEDDoNow For more info on how to use Twitter, click here. Do Now Do you make it a regular practice to care for the environment?

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Basic research shines light on parts of science we didn't even know we should be looking at. Image courtesy of Wikimedia Commons.

The budget proposal by the Obama administration is a mixed bag in terms of funding for science. Targeted research received some OK gains but basic research was left with the same or even less money than the previous year. If this trend continues, it won’t just be basic research that takes a hit. It’ll be your health and the U.S. economy too.

I know, I know, a scientist bemoaning a cut in funding — talk about someone with a vested interest! But hear me out.

In some ways this funding proposal is understandable. We have a dwindling pot of money and we want to fund what will be most likely to pay off. The problem is that this approach keeps science from finding completely new things that will lead to new approaches to treating diseases, identifying new energy sources and so on. We won't make any dramatic leaps in knowledge that fundamentally change how we address our problems.

Funding predominantly targeted research is like looking for your car keys only in lighted areas of the street. You are missing a whole lot places where the keys could be. Science is similar. Basic research is like adding new light posts—it opens up areas of research we didn’t even know we could explore.

I have a listed a few such findings off the top of my head. Because I’m more of a molecular biologist/geneticist, I’ve focused on these topics. There are undoubtedly lots of other examples from this and other areas that I haven’t included. Please feel free to add more to the comments section if you’d like.

Cell cycle regulators. Cancer happens when a cell grows out of control and/or refuses to die. Our cells have all sorts of controls in place to keep cells growing and dividing when they should and to also stop growing and even to die when they should too. The key regulators in this process were originally found in the humble baker’s yeast, Saccharomyces cerevisiae. We found them more easily in yeast because of the unique properties of this model system (easily manipulated genetics, fast growing, etc.). Because of that initial basic research, we were able to study this aspect of cancer and begin to identify treatments based on these regulators much sooner than we otherwise would have.

Micro RNAs. Until the early 1990’s, RNA was mostly thought of as a passive molecule. Basically the instructions found in genes in DNA were copied into RNA. This mRNA was then translated into proteins using two other RNAs, tRNA and rRNA, and it was proteins that did all the heavy lifting in the cell.

Through the work done in a small, see-through worm called C. elegans, we discovered that tiny RNAs are actually important in controlling how much protein gets made from a gene. These microRNAs are used in people too and have been shown to be involved in a number of cancers. Not only that, but they are incredibly useful tools for exploring how genes work so we can find new targets to go after for cancer research. It would have taken a very long time to find them with targeted research and even longer to figure out they were significant and how they work without basic research. I am not sure we would have found out what they are and/or do for decades if we had just focused on people.

Without the basic research on enzymes that cut bacterial DNA at certain places and the research on little bits of self-replicating DNA called plasmids, we’d still be getting our insulin from pigs and cadavers.

Genetic Engineering: What started out as some basic research on bacteria in the 1960’s and early 1970’s, turned into today’s genetic engineering. People who become anemic from cancer treatments can thank basic science for their EPO and people with diabetes can do the same for their insulin. Both are now grown in bacteria using the genetic engineering tools created from basic research.

And the list can go on and on. The human genome project has opened up so many avenues of research that we are still figuring out where to go with it all. The same is true for the basic research that identified stem cells, the structure of DNA, recombination and on and on.

If we had just focused on targeted research, we would have missed most of this or at least research would have been delayed by years or even decades. Sick people would have suffered longer because we didn’t fund basic research.

Of course I understand the quandary we are in here. If we have to choose between research on duck penises and food stamps for poor families, food stamps would undoubtedly win. This is even if the duck research might help us understand and possible even better treat conditions like preeclampsia, a problem with high blood pressure that can happen with pregnancy.

But we do need to think about how we can get the most bang for our limited science research dollars. Can we free up some money by streamlining how scientists are funded? Should we change how we assess whether scientific research has been successful or not? Should we divvy up the money in different ways with an increased percentage going to basic research?

I don’t have the answers to these questions but the folks in Washington need to start thinking about this. I don’t think we want to give up our strong science position in the world just yet.

More on applied vs. basic research

Importance of basic research

First-grader Hannah Chacko, of San Francisco, turned in this colorful drawing of the endangered San Francisco garter snake. (Perhaps a new t-shirt design for the city’s Sharp Park Golf Course?)

Foster City’s Kevin Huo, an eighth grader, submitted one of the most impressionistic entries in the bunch: this vivid depiction of an albatross – legendary protector of sailors — soaring above a boat.

The contest is sponsored by the U.S. Fish and Wildlife Service, the Endangered Species Coalition, the Association of Zoos and Aquariums and the International Child Art Foundation.

Top honors went to kindergartener Ava Bribiesco of St. Louis, Missouri, for her collage of the American Burying Beetle.

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.

Carl Sagan Poses with Model of Viking Lander

On Earth, evidence of past human civilization and habitation can be gleaned from the rocks, soil and some still-standing monuments of architecture large and small, but the effects over time of weathering and over longer periods of the geologic cycle tend to erode, erase and eradicate those past efforts.

But as a space-faring culture, we have now left our marks across the solar system on planets, moons, asteroids and in the empty space between them. Some of these “marks” are yet-functioning robotic spacecraft. Some are litter, scattered about the place like so many discarded soda cans, plastic grocery bags, depleted batteries and defunct electronic devices.

Are we trashing our solar system? Well, on the big scale of things, not much — and at present unavoidably. It’s a big solar system and the number of expended rockets, ejected parachutes, crumpled heat shields, empty fuel tanks and just plain expired or lost robots is quite small. And there’s no economically feasible means at present to clean them up. Besides, whose backyard are they littering?

As our surveillance of the reaches of our solar system grows more sophisticated, we are beginning to run across bits of “junk”. Don’t get me wrong, these are once important and highly useful equipment of exploration that we’ve left behind over the years.

Recently, the discerning eye on NASA’s Mars Reconnaissance Orbiter (the HiRISE camera) has spotted a couple bits of extra-Terran detritus.

Check this out: the discarded parachute of the Curiosity lander, flapping in the Martian breeze. I wondered where that ended up!

Luna 24, a robotic lunar lander from the 1970s, has been located through images by the Lunar Reconnaissance Orbiter. You can search for junk, too, at Moon Zoo.

And how about this Antiques Skyshow find: The possible last resting place of one of the first robots to land on Mars, the Soviet Mars 3 lander?

Some day in the future, when travel about the solar system is a routine vacationing activity, some of the sightseeing historical points of interest may be today’s space junk. I can imagine raised walkways and interpretive signs encircling the dust and wind scoured remains the long lost Beagle II lander on Mars, or the descent module of the Apollo 11 spacecraft on the Moon, or the Huygens lander half sunken in the super-frigid methane muds of Titan or the thoroughly scorched hulk of a Soviet Venera lander on Venus.

And imagine the Voyager and Pioneer spacecraft, coasting outward into interstellar space, one day serving as archaeological finds by alien species living in distant star systems, in the distant future, telling them that we are here—at least, were here, anyway.

What interests the geologist about the extension is that the rail line will cross the Hayward fault in two more places (BART already crosses the fault inside the tunnel between the Rockridge and Orinda stations). The Fremont Station, at the end of the line today, is just short of the fault. As you look south from the station, the fault comes from behind to the left and crosses to the right just across Walnut Avenue. Tule Pond, the little lake to your left, sits in a sag basin on the fault (learn more about them on the San Andreas Fault Trail across the Bay at Los Trancos Preserve).

The new track will cross the fault leftward, dive underground beneath Fremont's Central Park and re-emerge just north of the Irvington Station headed due south. It will cross the fault again, rightward this time, about where Washington Boulevard and Osgood Road meet. Here's the fault superimposed on a Google Maps image of the area.

Circles mark locations where evidence has been gathered on the fault. The red circle marks the Gallegos Winery site. Fault map from Lienkaemper (1992)

The low hill on the east side of Osgood is most probably a pressure ridge, the opposite of a sag basin, that marks the fault just like the pressure ridge in Hayward. Here's how it looks a little south of the station site; the Gallegos Winery was dug into it.

How the Irvington Station area looked in June 2009. All photos by Andrew Alden

The Hayward fault was attractive to builders before anyone understood faults. One reason is that faults often bring water to the surface; the other is that faults often build useful elevations in the ground. In Irvington, Juan Gallegos built a large state-of-the-art winemaking plant here in 1884 so that grapes could be loaded from the high ground in back and processed with the help of gravity. A rail spur served the front side, carrying thousands of barrels of excellent East Bay zinfandel to a ready market.

The three-story brick structure was a landmark much like its counterparts in Napa today, surrounded by gardens and palm trees. The building was destroyed by the 1906 earthquake (107 years ago today), but the land remained a garden estate, having been subdivided long before when phylloxera and a poor economy ended the good times.

Much later, the Hayward fault was mapped through here, and the abandoned site lent itself to scientific monitoring. One of the fault's four creepmeter installations is here. A creepmeter is a rod of quartz or Invar metal, securely mounted and housed in an underground climate-controlled vault that extends across the fault (see the plans here). It's regularly measured to track the slow, steady fault movement known as creep.

Solar power panel serving the Gallegos creepmeter

The creepmeter shows the fault here moving between 6 and 7 millimeters a year. The wall at the right side of the photo is also being bent by creep. Ideally, when the Irvington Station is built, this site will be spruced up and some interpretive signage put in. Fremont, unlike most cities along the Hayward fault, has done a lot to inform the public about it.

Once upon a time, Fremont was a celebrated wine district. It was good land, watered by thrust-faulted hills. If not for one or two accidents of history, today Fremont might be as prominent as Livermore and Napa as a wine region. Indeed, the whole East Bay could have made a superb viticultural region if the timing of its earthquakes had been a little different. Something to ponder with your aperitif.

Last week, scientists and regulators from more than 20 countries gathered in San Francisco to discuss the latest research on flame retardants. The conference lasted four days, but the theme of the meeting was clear from just a few talks: Do we need toxic chemicals to achieve fire safety?

For the past decade, scientists have voiced increasing concern about the potential health and environmental risks of these chemicals, which show up—and leach from—a growing number of consumer products. By now, most California consumers probably know that flame retardants permeate the foam in their couches and chairs, along with a surprising array of baby products. (On Monday, the San Francisco Chronicle noted that at least some nap maps sold in the state will no longer contain flame retardants.)

As I reported yesterday in a story for the Washington Post, mounting evidence suggests that these brominated chemicals pose risks to human health. Californians carry among the highest levels of flame retardants in the world, which researchers attribute to a 70s-era flammability standard that requires foam products to resist an open flame for 12 seconds. Manufacturers typically used flame retardants to comply and many tailored their products to California’s standard—and considerable market share—to avoid double inventories.

Gov. Jerry Brown, concerned about the risks the chemicals pose to human health, called on the state agency in charge of flammability standards to find a way to ensure fire safety without the need for toxic flame retardants. In March, the agency held a public hearing on its new standard, revised to do just that. The new regulations go into effect July 2014.

Since 2011, when I started writing about flame retardants, I’ve been struck by how the researchers studying these chemicals talk about their findings. Scientists tend to talk about their results in terms of what they don’t know and what new questions their studies raise. (All exceptions duly noted.) And those studying flame retardants do discuss their findings with all the usual caveats. But they also do something else. They tell me, "We don’t like what we’re seeing."

A few weeks ago, I spoke with Heather Stapleton, a flame retardant expert at Duke University who’s pioneered methods to correlate levels of dust on people’s hands with levels found in their blood or urine. With two small children, a four-year-old son and a daughter who will be two next month, Stapleton said she thinks very carefully “as a mother and scientist” about the products she buys and washes her children’s hands frequently to reduce exposure.

She’s particularly worried about people using hand-me-down nursing pillows and other baby products that likely exude more flame retardants as they age. “No one to my knowledge is examining infants’ exposure to flame retardants from these small items,” she said. “They’re small but an infant spends a lot of contact time with them.” What’s more, babies are likely to go from sleep positioner to a car seat to a changing table, spending the better part of a day in contact with products that could be leaching the chemicals.

Last week at the flame retardant conference, researchers talked about the global reach of these chemicals, now detected in trees, sludge, wildlife and people around the world. They listed the wide range of health effects associated with the well-studied brominated flame retardants—including endocrine disruption and developmental, neurological and reproductive defects—and emphasized that the effects have been found in both animals and humans. They also reported worrying early results on new formulations like tetrabromobisphenol A (TBBPA), which is showing up in human breast milk and maternal cord blood samples.

Historically, TBBPA was added mostly to electronics and circuit boards in a “reactive mode,” which means it’s unlikely to leach from the product. But as Linda Birnbaum pointed out at the meeting, it’s now being used as a replacement for banned or discontinued brominated flame retardants in an “additive mode”—so it can offgas, migrate from the product into the air. “Which means more is going to get into the environment,” Birnbaum said, “which means more is going to get into people and wildlife.”

Birnbaum, director of the National Institute of Environmental Health Sciences and the National Toxicology Program, reported that a two-year study of TBBPA in rats and mice found a dose-related increase in aggressive uterine tumors in the female rats—“these are highly malignant tumors that metastasize to many different sites,” she told the crowd—as well as liver tumors in male and female mice. These results suggest, she said, that TBBPA is a “two species carcinogen” that warrants closer study.

A few months ago, Birnbaum told me that she used to think flame retardants were providing fire safety but now isn't so sure. She allows there may be applications that warrant them, like airplanes, but even then, she said, “If we think flame retardants are going to be helpful, why not use them in a reactive mode, so they don’t easily escape into the environment?”

A decade ago, after seeing data showing rising levels of flame retardants in people along with animal evidence linking neurological effects to exposure early in life, Birnbaum called attention to the issue with a paper called "Brominated Flame Retardants: Cause for Concern?"

Now, she said, “everything that is being seen in people when you look—and until recently, no one looked—is consistent with things that we’ve seen in animal models.”

The weight of the evidence inspired Birnbaum to write another paper. “I changed the question mark,” she said, “to an exclamation point.”

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.

Many species of ducks come to the Bay to spend the winter. Photo by Ingrid Taylar

“The ducks would appear in flocks, darkening the air…” William Heath Davis; Yerba Buena (San Francisco). c. 1846.

Our winter ducks are getting ready to take flight for their summer breeding grounds. Subdued patterns have been replaced with vibrant breeding colors — for the males at any rate.  Any morning now, with the longer days and warm weather, we'll awaken and they'll have departed overnight.

Male ruddy duck attracting attention in full breeding plumage. Photo by Dick Daniels.

Scientists generally divide ducks into three categories: divers, dabblers, and “Sea Ducks”. Here are a few of my favorites starting with the diving ducks.  Ruddy ducks are built for underwater speed and agility, with their stiff tails used for steering underwater and large, webbed feet placed far back on their chunky bodies to propel them as they chase fish. Males are currently showing off their tawny red body feathers with bright blue bills set off against creamy cheeks. The females remain camouflaged brown with creamy cheek patches, good for sitting on nests unobserved. They’ll be migrating to Prairie Potholes soon where they’ll build nests in reeds suspended over shallow water.

Enchanting Northern pintail ducks remind me of graceful ballerinas. Their slim shape and longish neck — accented by a “racing stripe” of feathers on the males — and elegant head are the essence of refinement. The male’s tail, which have the longest tail feathers in the duck world, gives them their name. They seem to be continually enacting “Swan Lake,” including their habit of dabbling by tipping, butts up, to feed on underwater vegetation and insects. They’ll be migrating to freshwater ponds from California and northeast as far as Canada and Alaska. They nest on the ground in brush or grass where the female can sit camouflaged until the ducklings hatch.

A graceful male Northern pintail duck rests atop the water. Photo by Mehmet Karatay.

Striking buffleheads, identified by the large white patch on the back of the male’s head and white bodies, are in the group known as Sea Ducks. Though they’re small, buffleheads migrate to Canadian and Alaskan breeding grounds in aspen and boreal forests near lakes and ponds. A few isolated populations nest more locally. They seek out woodpecker holes 5-20 feet above the ground for their young and mates stay together for several seasons, which is unusual among ducks.

You can help with duck conservation by supporting efforts to maintain and restore healthy Bay habitats locally and nesting grounds further afield. You can also purchase "Duck Stamps", a surprising way to support ducks even if you're not a hunter.

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.

Here's the route along with the geology (made, as usual, with the help of the interactive state geologic map).

Great Valley Sequence rocks are upturned along the east edge of the Coast Range, increasing in age to the west: QPc, Quaternary-Pliocene continental sediment; E, Eocene marine rocks; Ep, Paleocene marine rocks; Ku, Cretaceous marine rocks. Qoa, aprons of old alluvium. The main valley floor is young alluvial sediment. The area east of Irwin is Ice Age sand from the Merced River. All photos by Andrew Alden

Drive through Patterson and get on Las Palmas Avenue. This may be the Valley's grandest allee of palm trees, although there's another one near Chowchilla you could see in another I-5 side trip. (Note to geologists: Turlock has an excellent brewpub if your trip calls for one.) Once out of town, you enter some of California's hardest-working farmland, based on excellent soils and abundant water.

South of Turlock, keep an eye on the roadside and notice as the soil turns sandy. Just below the "165" mark, you cross the Merced River, which is responsible for all that sand, marked on the geologic map by the lighter patch. Here Hagaman County Park offers a good view of the river, which still flows at a good clip all this way from Yosemite Valley. Notice, too, the levee north of the river, which keeps the annual floods from spilling wide over the countryside.

South of State Route 140 at the edge of the sand unit, the road crosses the San Joaquin River and enters the moist bottomland of the San Joaquin Valley. From here almost all the way to Los Banos is widespread tule marsh. Water is harvested from here and pumped to the San Luis Reservoir to regulate flow in the canals that serve the farms. That little squiggle of roadway west of 165 is actually the levee paths in Great Valley Grasslands State Park, a six-mile walk through a patch of the habitat that once covered vast stretches of the Valley. The path takes you along the San Joaquin River itself, much quieter than the Merced.

The grasslands include some vernal pools: shallow basins that fill with water in the winter and dry out slowly over the course of the spring, offering habitat for a great variety of plants and animals.

This winter was very dry, so the pools were not spectacular. As I walked I was reminded of William Brewer's description of this country exactly 150 years earlier: "We rode upward of thirty miles without any tree or bush—except once a single small willow was visible for two hours, but we passed nearly two miles from it; it was a mere speck. Hour after hour we plodded on. The road was good but a dead level—no hill or ridge ten feet high relieved the even surface—no house, no tree—one hour was but like the next—it was like the ocean, but it depressed the spirits more." But then I spotted a nice patch of goldfields and gave my camera a treat.

In Los Banos, the Los Banos County Park just a few blocks west on route 152 has a museum, as well as bathrooms and shade.

"Los Baños" means "the baths," and it got its name from the clear pools in Los Banos Creek where it leaves the Coast Range, so refreshing to Father Arroyo in the Mission days that he made a point of returning regularly. Today everyone has bathtubs and it's hard to imagine being excited by such a thing. Father Arroyo's baths were soon erased as the creek was dammed, an early step in the immense and still incomplete project of harnessing and managing California's water. Los Banos Creek Reservoir is just west of the lowest I-5 symbol on the map.

The steep face of the Laguna Seca Hills, eastern rampart of the Coast Range, looms as route 165 approaches the freeway again. Along the road you may notice long piles of white rock.

Pull over and take a look at some. It's diatomite, a styrofoam-light rock made exclusively of microscopic diatom shells.

This material testifies to a long-lived, quiet brackish or alkaline lake that existed here millions of years ago. Different accidents of tectonics have turned the Valley, at various times in the geologic past, into a freshwater lake, an inland sea or a dry desert.

The quarry that yields this material is up in the Laguna Seca Hills just behind this view; you can see it in Google Earth.

The state geologic map shows that the Laguna Seca Hills expose an unusually complete and compact cross section of the Great Valley Sequence. If only we could access the rocks! But it's private land, and anyway here's the freeway again.

Using a common DNA ancestry test, President Obama would be 100% Caucasian.

Sometimes genetic tests aren’t as useful as you think they will be. For example, if President Obama were to take a common ancestry DNA test, it would almost certainly come back as 100% Caucasian. Useful, huh?

This sort of test, a mitochondrial DNA (mtDNA) test, can look into the deep past but it can only see mom’s side of the family. And it isn’t even really that powerful. It not only ignores dad’s side of the family, but in reality it can only see a sliver of mom’s as well.

So with this test you can see your mom and her mom and her mom’s mom and so on. You can also see your mom’s sister and her kids and your grandma’s sister and her kids. What you won’t see, though, is your mom’s brother’s kids or your grandma’s brother’s kids or any male relative’s on your mom’s side of the family. It really only follows back a direct, specific maternal line.

This is why President Obama would look Caucasian in this test…because his mom is Caucasian. Now of course with a little knowledge about these sorts of tests, President Obama wouldn’t be surprised. But not everyone knows they have a relative on their direct maternal line who is of a different ethnic group.

I know of a case where a self-identified African-American woman had a mtDNA test done to try to determine what part of Africa her ancestors came from. Apparently they came from Europe; her test came back 100% Caucasian. This is despite the fact that all her living relatives were African-American and no one can remember any relatives who were Caucasian.

As this result shows, we don’t have to come up with an explanation like President Obama’s—it doesn’t have to be that her mom was Caucasian. Because of how these tests work, the DNA from this test could have come from a woman five, ten or even fifty generations back. Mitochondrial DNA passes from mother to child virtually unchanged, generation after generation.

What this means is that there is no dilution of mtDNA as the generations pass. Mom’s mtDNA is pretty much the same as grandma’s which is pretty much the same as great grandma’s and so on. This DNA doesn’t dilute over time.

Here is one way to show what might have happened to this woman’s DNA over the generations:

In the diagram, circles are women and squares are men. Also, white means Caucasian and black means African.

On the left, we are following the mtDNA of the tested woman and on the right we are following the rest of her DNA. She is the circle at the bottom of the family tree on each side.

What you can see on the right is that over the generations, the original Caucasian DNA is being diluted out. It goes from 50% to 25% to 12.5% and so on as you’d expect. The same isn’t true for the mtDNA on the left. It stays Caucasian generation after generation.

So if we look at most of her DNA, she looks African-American. We may not even see that sliver of Caucasian! But her mtDNA is 100% Caucasian. No wonder she was confused.

Obviously she can’t find out what part of Africa her ancestors came from with this test. But let’s say she got a more typical result and her mtDNA could be traced back to some part of Africa. What does that result really mean?

As the result here shows, it may not mean as much as she hopes. Imagine the previous scenario but instead of being Caucasian, the woman from five or ten generations ago came from a different part of Africa than the rest of her relatives. She would come away thinking her relatives were from one part of Africa when most of them were really from another.

She would not get the answer she was looking for but there is no way for her to know she got the “wrong” answer. She would simply go on believing she was from a part of Africa she really wasn’t.

Unfortunately, there really isn’t a better DNA test for looking back in time. The most useful tests, the autosomal ones that look at all our DNA, can only go back four or five generations before becoming hopelessly jumbled. For most African-Americans, this isn’t far enough back to find their African ancestors.

The other kind of test, the Y chromosome test, can go as far back along the paternal line as the mtDNA test can along the maternal line but it suffers from the same problems. In fact, a surprising number (35%?) of African-American men actually have Caucasian Y chromosomes (well, given plantation life, maybe not so surprising). None of these men will learn anything about their African heritage with this test.

So the bottom line is don’t put too much faith into DNA testing alone. It is kind of fun to trace back your history this way but you are really only following one strand of your ancestral web back in time. The rest of the web is invisible to DNA testing.

Of course mtDNA tests have been incredibly useful scientifically. They’ve let us trace human migration as we spread out of Africa and even trace all of our lines back to a single woman, Mitochondrial Eve. Recently these tests were even used to confirm that a skeleton found under a parking garage in England belonged to King Richard III.

Just don’t count on mtDNA tests giving you a broad understanding of your own family history. They won’t.

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.

Image of sun through a Sunspotter Telescope

Thinking back through my life, I recall four times when I took notice of sunspots one way or another.

Back in 1980 when I was in the 12th grade, I remember seeing them in solar images I projected from my 4-inch Astroscan telescope.

Then in 1991, when I worked in an aircraft hangar at NASA/Ames Research Center, I remember walking by a disk of light on the floor and realizing that it was an image of the sun projected from a hole in the hangar roof—making the entire hangar a giant pinhole camera. The disk was several inches across, and in it I saw sunspots once again.

In 2002, around the time that I started working at Chabot Space & Science Center, I made a regular activity of sharing the spotty sun with visitors, teachers, and summer camp kids alike, using Sunspotter Telescopes, pinhole projectors, and filtered telescopes. Again, the spotty sun was raised in my awareness.

And now in 2013, we have spots once again!

The pattern was always there for me to notice: 1980, 1991, 2002, 2013. See it? I didn't, until in recent years, because noticing the regular pattern of the appearance of sunspots over time requires that you notice the times when the sun isn't so spotty. During those times, the sun simply fell from my attention because there wasn't much to see.

If you've been following the sun lately, you're aware that we're somewhere in the midst of Solar Maximum: that season in the solar cycle of greatest magnetic activity when sunspots and other related magnetic events like solar flares and coronal mass ejections are frequent and pronounced. On average, Solar Maximum comes every 11 years, reaching a singular high in magnetic activity and then relaxing toward Solar Minimum. By the original predictions, Solar Maximum was expected to peak around May of 2013.

However, except for a sharp spike in activity in late 2011, all of 2012 fell below par, appearing on graphs as if Solar Maximum climaxed a year early and is now on the way out.

Did it fizzle, ending unexpectedly early — and after a performance that fell short of the anticipated mark?

Or perhaps…with a light drum roll…is the drop in activity we've observed lately only a brief calm before a spectacular resurgence?

While some have suggested that we have experienced a tepid Solar Maximum that simply didn't meet market expectations, another explanation is afoot: the sun is getting ready to deal out a "double peak" Solarmax, with the second peak getting ready to ramp up.

If this is the case, Solarmax has yet to give us its finale fireworks display, which we could expect later this year and perhaps crackling on into 2014.

A double-peak Solar Maximum isn't a novelty, as it turns out. In fact, the last two of them (back in 2001/2002, and before that in 1990/1991) exhibited similar behavior. Why? We're still working on the answer to that, but the double-tap maximum may be a result of the sun's two hemispheres, north and south, reaching Solar Maximum at slightly different times. Currently, it appears that the sun's southern hemisphere is lagging behind the north in activity—and maybe getting ready to make up for lost time.

If you're wondering what all this magnetic activity on the sun actually looks like, come up to Chabot Space & Science Center and see for yourself. Our new exhibition, "Touch the Sun" features fully interactive movies of solar activity on a 90-inch color television.

Photo by Rachael Rufino

Peregrine falcon (Falco peregrinus) nest cameras in San Francisco and San Jose have been giving citizens the unique chance to watch these animals up-close since 2005. Because this species was nearly extinct in the 1970s — with only two pairs left in California — it is a real thrill to see them thriving alongside humans today.

According to the University of Santa Cruz Predatory Bird Research Group (SCPBRG), the San Jose pair "Carlos" and "Clara" have experienced a relatively smooth breeding season. Clara was documented laying the first egg of the season February 19th, and a fourth egg on March 4th. The first egg hatched on Easter Sunday, March 31st! By Monday, three chicks were present.

Photo by Rachael Rufino, Courtesy of SCPBRG San Jose Nest Cam

With large concrete buildings in urban areas resembling natural cliffs, peregrine falcons have been drawn to nest each year at San Francisco's PG&E building and San Jose City Hall. Although San Francisco's nest site regularly gets media attention, few people know that the San Jose falcon pair is actually easier to see on foot. With a more open landscape, the corner of 4th and San Fernando Street is recommended for viewing.

Like all falcons, peregrines specialize in hunting other birds, and Carlos and Clara will soon have to hunt for their growing brood. In urban areas, pigeons and blackbirds are a primary food source. Peregrines have very large feet for their body size to grab birds in midair and a "tomial" tooth, which is a special notch in their beak to sever their prey's spinal cord. In addition, they are the fastest animal on the planet, with one peregrine clocked at diving 242 mph to catch prey.

After hatching, the parents will continue to stay on the nest for another week. In roughly three weeks, SCBRG researchers will place leg bands on the chicks that will help identify individuals. Shortly after, the chicks will begin learning how to fly. This is the most dangerous time of any flighted bird's life, and learning how to fly in an urban environment with cars and people can make it even more difficult. In about six weeks, the chicks will be independent and perhaps find an urban nesting site of their own.

Tropical glaciers are few, scattered and endangered. South America and the Himalaya have most of them, and nearly all have been shrinking rapidly for several decades. Professor Lonnie Thompson of Ohio State University has specialized in drilling ice cores from them for more than 30 years, and the very first one he cored, in 1983, is a remote ice cap south of the equator in Peru named Quelccaya whose top sits above 18,000 feet. There he pioneered the use of a lightweight, solar-powered drill rig and succeeded in collecting two complete cores through the ice, about 160 meters long. Unable to keep them frozen, he had to cut them into sections and let them melt, then brought the water home in bottles.

The Quelccaya ice cap, 12 kilometers across, is the largest icefield in South America. Google Maps image

Twenty years later Thompson returned and brought two new cores, intact this time, to Ohio State's ice locker. In a paper published today in Science, Thompson's team shows that the 1983 and 2003 cores faithfully preserve a year-by-year record of tropical climate 18 centuries long, extending back to the year 683 with annual resolution and a little less perfectly back to almost 200. Thompson calls it "the longest and highest-resolution tropical ice core record to date."

The possibility of retrieving such precise records was what excited Thompson from the beginning. The ice consists of spectacular annual layers that represent dry winters and wet summers. The winter layers collect the lion's share of the year's dust and dissolved chemicals while the summer layers represent rainwater from the Atlantic Ocean, filtered through the tropical Amazon basin.

Annual layers in the Quelccaya ice cap are about 75 centimeters thick. Lonnie Thompson photo

The data from the Quelccaya cores shed light on many scientific problems related to climate. Most notably, the extent of summer snow from the east depends strongly on Pacific Ocean influences from the west, such as El Niño cycles—so strongly that the Atlantic snow record shows us the temperature of the Pacific as if in a mirror. And Pacific sea-surface temperature is one of the most important numbers in the planetary climate because it's the best gauge of how much water vapor enters the atmosphere.

Central Pacific sea-surface temperature (SST) during the last 1800 years reconstructed from the oxygen-isotope record of Quelccaya ice. Image from Science

The climate record in the Quelccaya cores gives us the nearest thing to real truth in the centuries before modern science. It helps sharpen the picture provided by other ice cores, especially those in the tropics. And that in turn makes global climate records, and the models built upon them, more robust as we peer into the past and future.

We have little time to waste. Thompson's latest expedition to Quelccaya documented hundreds of meters of shrinkage since his first visit. Newly exposed plant remains at the glacier's retreating edges were found to be 6000 years old. And the top layers of ice, deposited since Thompson's first visit, show signs of summer melting for the first time in the entire record.

"Cypress Swamp, Alligator Bayou, Prairieville, Louisiana" (negative 1998, print 2012) Injet print by Richard Misrach. High Museum of Art, Atlanta.

In February 1970, in a special message to Congress, President Nixon served notice that American corporations had laid waste to the country’s land, air and water resources long enough. “We in this century have too casually and too long abused our natural environment. The time has come when we can wait no longer to repair the damage already done.”

Before the year was out, Congress authorized the Environmental Protection Agency to establish and enforce standards to protect the environment. Forty-three years later, it’s hard to think of a place where that mission has failed more miserably than Louisiana’s Cancer Alley.

For the 85 miles between Baton Rouge and New Orleans, the haunting swamplands of the Mississippi River corridor—called America’s wetland for its biological value to the nation—bump up against the sprawling refineries and paraphernalia of the petrochemical industry. Industry leaders call this stretch of the Mississippi, sandwiched between 150-plus oil and gas plants on both sides of its devastated banks, Chemical Corridor. But locals—who blame the millions of pounds of toxic chemicals pouring out of industry smokestacks every year for high rates of miscarriages, cancer, respiratory ailments and other serious diseases—have another name for it. They call it Cancer Alley.

In 1998, Richard Misrach went to Cancer Alley to produce a series of photographs for an exhibition commissioned by Atlanta’s High Museum called “Picturing the South.” Misrach, known for penetrating portraits of human disturbances of the natural landscape, returned last year at the High Museum’s request. The museum displayed his new photos alongside the old series last year.

"Swamp and Pipeline, Geismar, Louisiana" (negative 1998, print 2012) Inkjet print by Richard Misrach. High Museum of Art, Atlanta.

Now you can see what’s changed—or not—in “Revisiting the South: Richard Misrach’s Cancer Alley” at Stanford University’s Cantor Arts Center.

Like any great artist, Misrach mines the troubles of his times—in this case, environmental devastation wrought by an petroleum-based economy—to raise broader questions of human existence. As you walk among the large-format photos, most measuring 6 feet by 5 feet, it’s hard not to get drawn into the destruction. Their imposing presence echoes the scale of the waste and brings us in intimate contact with it. Now that we see the consequences of our dependence on oil, what will we do to restore what’s been lost? If we do nothing to repair this ecological ruin, are we as guilty as the polluters?

I seemed to find my answer in “Holy Rosary Cemetery and Dow Chemical Corporation (Union Carbide Complex), Taft, Louisiana,” (1998): Dark clouds linger heavily over an industrial facility that serves as backdrop to a cemetery that once adjoined a church. But it is Jesus looming on the cross that catches your eye. Is he paying for our environmental sins? In the photo’s label, Misrach notes, “Dow (which now owns the complex) leaked 26,720 pounds of vaporized ethyl acrylate (EA), a Class II toxic air pollutant, into the atmosphere. No fine was levied, but Dow has pledged a $100,000 contribution to the Surpriya Jindal Foundation for Louisiana’s Children…).

"Night Fishing, Near Bonnet Carre Spillway, Norco, Louisiana" (negative 1998, print 2012) Inkjet print by Richard Misrach. High Museum of Art, Atlanta.

Most residents of Cancer Alley are poor and African American. Misrach makes sure you don’t miss the legacy of racism that has long plagued these communities, with “Restored Slave Cabins, Evergreen Planation, Edgard, Louisiana” (1998) and “Tour Guide, Nottoway Plantation, White Castle, Louisiana” (1998), showing an African American woman peering through the window in the grand foyer of an old plantation. Here, plantations persist among the petrochemical plants, and the specter of past injustices hovers over modern human rights violations, where all communities do not receive equal protection from environmental hazards.

There is no doubt that Cancer Alley is one of the most polluted regions in the United States. Less clear is what explains the high rates of cancers afflicting the community. It’s notoriously difficult to link cancer clusters to any particular exposures. Misrach seems to capture that ambiguity in several photographs—a hazardous waste site, a parking lot and a pipeline above a murky river, all shrouded in a dense haze. Is the haze just fog or is it a toxic chemical cloud?

In some cases, labels remove any doubt what the haze is meant to imply. In “Hazardous Waste Containment Site, Dow Chemical Corporation, Mississippi River, Plaquemine, Louisiana” (1998), you’ll learn: “Between 1958 and 1973 Dow buried forty-six thousand tons of toxic waste in unlined pits that now cover more than thirty underground acres. The company attempts to pump the waste back to the surface before it reaches the drinking water aquifer for the city of Plaquemine.”

You’ll leave wondering how anything could survive a decades-long onslaught of toxic releases into the land, air and waterways in such a concentrated area—and how the EPA could allow the poisoning to continue for so long in such an ecologically sensitive area with a long history of racial injustice.

Revisiting the South: Richard Misrach's Cancer Alley: Photographs. Through June 16. Cantor Arts Center, Stanford University, Stanford. (650) 723-4177.

Photograph of the Cefaly anti-migraine device courtesy of STX-Medsprl via Wikimedia Commons licensing.

Perhaps this has happened to you: while grocery shopping at your local supermarket, suddenly your peripheral vision begins to disappear. This could be frightening, but you know what is coming: a one-sided pulsating pain, sensitivity to light and noise, nausea, vomiting and seeing flashing lights. You quickly drive home and cancel your plans, because you have a migraine headache coming. You need to lie in a dark quiet room for the next 24 hours, trying to move as little as possible.

Migraines affect about 30 million Americans, most commonly between the ages of 15 and 55. This means that one in four households in the U.S. have at least one member impaired by migraines. Women are three times more likely to be migraine sufferers than men.

Unfortunately, there is currently no cure for migraines. A migraine diary can help identify the headache triggers to avoid. Medications can also help reduce the number of attacks or ease the symptoms, such as painkillers, Triptans (that cause blood vessels in the brain to narrow), anti-inflammatory medications, anti-nausea medicines or feverfew herb. However, these medications are often ineffective or cause unpleasant side effects.

Instead migraine sufferers might find relief from a new non-medicinal alternative, a device called a supraorbital transcutaneous stimulator (STS) that stimulates the nerves around the eyes and forehead. A study recently published in the peer-reviewed journal Neurology tested the safety and effectiveness of this STS device designed to prevent migraines.

Conducted by researchers in five specialized headache clinics in Belgium, this study was a randomized controlled trial that compared the STS device with an identical-looking sham device. Study participants were aged 18 to 65 who routinely experienced a minimum of two (average of four) migraine attacks per month. None of the 67 participants had taken anti-migraine medications in the three months leading up to the study.

Both the STS and sham devices used self-adhesive electrodes placed on the forehead, covering the bridge of the nose and above both eyes, that buzzed identically during treatment. Only the STS devices delivered electrical impulses. The participants wore one of the devices for 20 minutes per day for 90 days.

The participants’ migraine diaries indicated that the STS device reduced the number of migraine days per month from 7 to 5, while the sham group experienced no significant difference. In addition the number of migraine attacks dropped by at least half for 38% of the participants using the STS device, compared with 12% for those using the sham device.

Although the severity of the migraines was not reduced, people using the STS device had fewer days with headache, fewer total migraine attacks and used fewer pain relief medications each month. Most importantly, there were no adverse effects seen in either group.

The study concluded that treatment with a STS device is “effective and safe as a preventive therapy for migraine.” The Ceflay anti-migraine device kit is now available for $240-$300. However, only 67 migraine sufferers have been studied and the use of this device was only examined for three months. Larger studies with longer-term treatment are needed to confirm that this STS device is safe and effective.

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.

A Bufflehead mounted specimen provided an opportunity for students to examine a bird up close.

Her voice rang out over the excited young artists, “Who knows what ‘nurture’ means?”  Small hands shot up in the air, anxious to share their new knowledge.  Two kindergarten classes from Maya Lin in Alameda, a new Arts Magnate School, were here to participate in an art and science field trip.  Ginny Parsons is an Environmental Artist with her work currently featured in the “Nurture/Nature” exhibit at Rhythmix Culture Center in Alameda.  Her large canvases and found-board paintings line the walls of K Gallery, where the students were gathered.  Her paintings feature dense habitats, textured and layered with beeswax and bacon grease. They’re populated with large-scale, evocative depictions of shorebirds, pelicans and falcons.

Students looked through a spotting scope to see live birds up close. Photo by Janet Koike.

After Ginny’s introduction to the process of creating art and more specifically, environmental art, it was my turn to lead a short bird walk with the students from the art center to the Estuary waterway behind the Bridgeside Shopping Center.  Students used a spotting scope and binoculars to observe cooperative coots and gulls on the docks and pilings.  The young observers noted the red eye and white bill against smooth, black feathers of the coot.  They applauded when a brown pelican dove headfirst into the salty water with a splash. Feeling inspired, we headed back to the art studio to work with magazine pages and oil crayons. Ginny had each child create their own unique piece of artwork to take back to school. Their teacher explained the outing followed their classroom studies about habitat.

There are new movements afoot to bring together art and the environment throughout the U.S. and even some here, closer to home.  There’s an interesting school in Philadelphia, the Schuylkill Center for Environmental Education with an Environmental Art Department.

Young environmental artists at work.

They note, “using art as a tool to understand nature, and nature as a framework to understand the elements of art…offer(s) a fun, innovative and effective paradigm for studying the natural world and visual language.” Closer to home, Ginny Parsons will be hosting a “Make It Workshop” this weekend at Rhythmix (reservations required) and then an Earth Day workshop at the Alameda Free Library. Families can also participate in the annual Sandcastle and Sculpture Event at Crown Memorial State Beach held one Saturday each June.  Additionally, for the last couple of years in September, an “Art in Nature Festival” has been held in Redwood Regional Park. A favorite Andrew Goldsworthy-esque play area remains in the park after the last festival where you can create with natural materials along the edges of a trail through a young redwood stand. You don’t have to be adept at art or drawing to use your powers of creation to get a new perspective on nature!

Hikers and bicyclists will be thrilled with the high views up and down the coast. They may feel a tickle as they look at the surf hundreds of feet below. And some of them will feel curiosity as they look inland at the sides of the road, about 1.3 miles of it, that they could never stop and see before.

This stretch of road passes through two very different sets of rocks. The south end is the granite of Montara Mountain; I showed you some of this at Quarry Park in El Granada, a bit farther south, in 2011. It holds up the rugged headlands around the tunnel's mouth. It dates from Cretaceous time, just like the granite in the Sierra Nevada—and in fact it's the same stuff, ripped out of the range and pulled northward here by the San Andreas fault. The same granite is found as far north as Bodega Head and south to San Luis Obispo County (including Pinnacles and Fremont Peak, part of a sliver of tectonic plate that geologists know as the Salinian block.

Caltrans

The north end is a thick pile of mudstone that dates from Paleocene time, slightly younger than the granite. This is the material that gave Devil's Slide its name. It's been falling into the sea for untold centuries, including the last century in which we have been vainly putting roads across the cliffs.

Caltrans

The San Mateo County geologic map describes it as marine shale and sandstone with beds of conglomerate. The conglomerate is basically sandstone that includes "angular boulders of granitic rock as long as 2 meters and smaller boulders, cobbles, and rounded pebbles of hornblende gneiss, muscovite gneiss and schist, Franciscan chert, quartzite, limestone, sandstone, and shale." That variety of material represents a long-vanished countryside rather like today's, with vigorous rivers that carried this coarse sedimentary material straight out to sea.

The contact between the granite and the mudstone is an inactive fault. Both units are in the Salinian block. And now it's time to show them on the geologic map.

Major units: Kgr, granitic rocks of Montara Mountain; Tss, Paleocene sandstone and shale; fs and fg, Franciscan sedimentary rocks; blue, Franciscan limestone. The "V" signs mark the tunnel entrances.

That fault contact will be an attraction for many geologists and students. Local researcher Kathleen Burnham describes what she looks forward to seeing here: "Among the notable features now hazardous and difficult to access are bedding-plane trace fossils, vertical burrows filled with white carbonate, some isoclinal bedding folds, and the contact between the strata of Point San Pedro and the underlying Montara Granodiorite. The Devil's Slide project as a whole will greatly enhance accessibility of these spectacular outcrops when the project is finished, traffic diverted, and vehicles no longer whizzing by within inches."

The geologists at Caltrans have been good friends of the geological community. Now that the old roadbed is in the County's hands, let's hope they don't decide to hide these rocks. Who knows how long we have to enjoy them.

The first fully automated 3D printing vending machine is open for business at UC Berkeley's Etcheverry Hall. In the background, Richard Berwick, Dreambox co-founder and chief technology officer, makes some adjustments to "Dolly," the prototype's nickname. (Sean Greene/KQED)

Combining 3D printing technology with the convenience and accessibility of the DVD-dispensing Redbox service, student entrepreneurs at UC Berkeley have built a vending machine with a seemingly infinite selection of products.

The Dreambox, which now lives in the campus’s Etcheverry Hall, is the first fully automated 3D-printing vending machine, representing a step forward in the democratization of the still-young technology.

You can print almost any object using its touchscreen and watch said object materialize before your eyes. When the print is complete, a mechanical arm will push the object into a locked drawer for safekeeping until you pick it up. The Dreambox can print model cars, whistles and even a detailed miniature of UC Berkeley's iconic clock tower, the Campanile.

While 3D printers have been around for years, their use is primarily restricted to academic or industrial environments. At Cal, Dreambox customers can print their own preloaded designs such as dog tags, snowflakes or cups, or choose from thousands of items on the digital design repository, Thingiverse. Customers can even bring in their own computer-aided design (CAD) files for printing.

"Some of them are useful, some of them are decorative," says Richard Berwick, a recent graduate from the Haas School of Business and Dreambox chief technology officer.

The possibilities would be endless, if it weren’t for the 7-by-9-by-5-inch size restraints of what Dreambox can print.

In Dreambox’s office at Berkeley Skydeck, the university’s technology startup accelerator, Berwick, along with his co-founders David Pastewka, the CEO, and Will Drevno, COO, were fixing some final glitches with "Dolly," the vending machine’s nickname.

The Dreambox, nicknamed Dolly, is the first fully automated 3D printing vending machine. Customers can select an object or enter their own design, and watch it print before their eyes. (Sean Greene/KQED)

Dolly is a large cabinet sitting on two wooden furniture dollies. She weighs more than 400 pounds and has a plexiglass face so people can watch her 3D printer in action.

A table shows off some of Dolly’s early colorful successes and some failures. There’s a red rocket ship shot glass, a yellow infinite knot and a solid plastic iPhone 5, the result of an incorrectly exported CADD file.

The largest item is an unbreakable plastic I-beam, an elongated letter-shaped object similar to steel beams used in construction, printed by engineering students testing Young’s modulus. “You can throw it on the ground if you want, it won’t break,” Berwick said. It didn’t.

Members of the campus community already have their own ideas for what they’d like Dreambox to print.

Customers have printed architectural models, items from video games and even the body and wings of a drone plane. Now the thing zips around at 4 meters per second. Fraternities and sororities have asked Dreambox to print custom shot glasses. So far, Dreambox has completed more than $1,000 in prints, and could be profitable in a matter of months if it’s used at full capacity.

Berwick said the co-founders have no plans to restrict what customers may print, except for weapons. But then Berwick recalled a 3D printing pop-up store in New York that soon turned into a “custom” sex toy shop.

“That’s not something we can say we’re necessarily OK with,” he added.

The Dreambox uses an “off-the-shelf” 3D printer, worth about $2,200, and prints from colorful spools of polylactic acid (PLA), a corn-based biodegradable plastic. So the Greeks’ custom shot glasses would be safe to drink from, at least according to the material safety data sheet, the founders said.

“If you put it in the oven, it will melt into a puddle,” Berwick says. “If you put it in the microwave, it will also melt and possibly spark.” Definitely don’t put it in the dishwasher.

In some cases, the machine’s entertainment value is almost better than the quality of its products, Pastewka said. People uninterested in the product will still watch the printer head move back and forth, back and forth. “No blinking. I’m sure I’ve done the same thing,” he said.

The Dreambox 3D prints a miniature version of UC Berkeley's iconic Campanile Tower. (Sean Greene/KQED)

Berwick started a test print: a smaller, simpler model of the Campanile Tower.

The platform and printer heads whir to life as the chamber heats up. Then, 270 micron layer by 270 micron, layer at a time, our very own four-inch tall Campanile materializes. Fifteen minutes later, it’s done, but something’s not quite right. The top, which should be a perfect pyramid, is misshapen and, well, melty.

Berwick says the model was too small and the chamber too hot. A reprint might be in order.

Pastewka said the Dreambox machine on campus is just a prototype, “the first instance of what could be a lot more.”

“We’re proving something here,” he said. “A lot of people are watching us to see what happens. I’m reading an email from someone in Turkey. A lot of people have some interesting ideas what this could do. Some of them are unrealistic, but interesting.”

The Dreambox is now open for business, with print costs ranging from $3 to $15. The machine lives in Etcheverry Hall, 2521 Hearst Ave. in Berkeley.

The Devil's Slide Tunnels south of Pacifica and north of Half Moon Bay are finally opening after decades of environmental battles and years of construction.

The tunnels are meant to solve the safety and erosion problems that have plagued that notorious stretch of Highway 1 since it was built.

The new tunnel consists of two bores each about 4,200 feet long and each 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.

A couple hundred people turned out for today's ribbon cutting ceremony including Congresswoman Jackie Speier and the wife and daughter of the late Congressman, Tom Lantos whose lobbying efforts help lead to the construction of the new tunnels. Also present at the opening ceremony was the Half Moon Bay High School marching band and a number of environmental activists who pushed for the tunnels.

Environmentalists who had agitated for the tunnels, instead of a highway bypass, are known as "tunnelistas." Among them was Ann Forrister, who was there under an alias, “My name is Captain Tunnel, and I am wearing red tights, black shorts, a red cape, tunnel vision glasses, a red hat. I'm celebrating the tunnel”

A parade of antique cars were the first vehicles to drive through the new tunnel.

Pacifica resident Mike Mooney holds a picture of himself next to a stretch of Devil's Slide during one of the more memorable highway closures.

Two new bridges connect Highway 1 to the tunnels and bypass red-legged frog habitat in the valley below.

The 439-million dollar tunnels are the first to open in California in nearly fifty years and are the longest tunnels in the state. CalTrans plans to open the tunnels to traffic tomorrow morning.

As for the old stretch of highway with breathtaking views? It will soon open to hikers and cyclists.

This video shows a CalTrans bus carrying select members of the public and media driving through the west tunnel. The footage is sped up and does not show the entire length of the tunnel; it focuses on the entrance and exit.

Andrea Kissack contributed to this report. Photos and video by Jenny Oh.

Someday we might be able to resurrect some of these long extinct species. The species depicted here have all become extinct since the mid 1700s and the colonization of the New World. Part of the painting GONE from 2004, 4'x3', oil on canvas painted by Isabella Kirkland, artist and research associate at The California Academy of Sciences.

There has been a lot of buzz of late about bringing back extinct species like mammoths or passenger pigeons. While it might be a good idea to start thinking about these possibilities, we are years or even decades away from being able to actually pull this off with most long dead animals.

The problem isn’t reading the DNA…we are actually getting pretty good at that. And the problem isn’t even making the DNA. It would be quite a stretch to make a complete set of mammoth DNA but with a lot of time, money and effort, we could probably do it.

No, the real problem is getting a cell to read any DNA we make in the lab. See, DNA has to be folded just so to fit inside the cell and we simply cannot do this on our own yet. And when you think about the proportions of what we’re dealing with, it becomes pretty obvious why we can’t.

An animal’s DNA is stored in the nucleus inside the cell. A human has six feet of DNA in each cell and the average nucleus has a diameter of about six micrometers. So the cell manages to stuff two meters of DNA into this tiny space.

To give you an idea what we’re up against, imagine the nucleus is the size of the average baseball, almost three inches in diameter. If our nucleus were this big, we’d need to cram 75,000 feet or 14.2 miles of DNA in there. Talk about a daunting challenge!

We can’t just force it in either. We need to fold it perfectly to make sure the right genes are in the right place to be turned on properly. The DNA has to be twisted around little spools called histones and then twisted and folded and twisted some more until you get the nice compact shape of a chromosome.

Right now, only a cell can pull this off and until we figure out how to get lots of manmade DNA into a cell to have the cell fold it for us, we are stuck cloning with living or properly frozen cells. We simply don’t have this kind of material for most extinct animals. But we do have frozen cells for a few.

For cloning to work right now, you need to start with an intact cell. We have this for the extinct Pyrenean ibex.

One likely candidate for resurrection is the Pyrenean ibex. Scientists managed to collect and save cells from the last of these wild goats before she died in 2000. These cells are now being used to try to bring this goat back.

Basically, as outlined to the right, scientists first replace the nucleus in a goat egg with a nucleus from the ibex. This won’t grow and develop properly because the ibex DNA is configured to be used by an adult cell. So the next step is to use chemicals and/or electricity to reconfigure the DNA to be useful to an embryo. Then this “fertilized” egg is grown a bit, placed in a surrogate mother goat and then, if everything goes well, the species is reborn.

So far things have not gone that well. The tricky part in this is reconfiguring the adult DNA into embryonic DNA. If this isn’t done just right, the embryo won’t develop correctly. And finding the right conditions is done by trial and error and is different for different animals. What this means experimentally is a lot of failed pregnancies and a lot of sick and dead baby goats before hitting on the right conditions.

This might be acceptable in this case to bring the goat back but maybe again it isn’t. Are lots of goats dying early, horrible deaths worth bringing back the ibex? I don’t know.

The question gets even harder when we are dealing with mammoths. Here we need to do more experimentation either because we need to try to get the DNA folded correctly or we need to get useful nuclei from cells frozen improperly in the Siberian tundra for thousands of years. Either way, we are going to have many more failed pregnancies and dead baby mammoths.

Remember, the surrogate here will be an elephant. Elephants are smaller than mammoths and have a gestation period of nearly two years.

At first the gestation period won’t matter because the failed pregnancies won’t go very long. After hundreds or thousands of failed pregnancies, scientists will have tweaked the conditions enough so that some mammoths will get closer to birth and eventually even be born. Now we’ll have to wait a couple of years to see how our new conditions worked and to make the next tweaks.

This all gets a lot more horrible if a mammoth baby is too big for an elephant to deliver naturally. If they are, we’d either need to have them born prematurely or do something like a C-section on the surrogate mother. This all sounds like a nightmare.

It was troubling enough thinking about all those dead and deformed goats but elephants are a whole different matter. In this scenario, these intelligent, caring animals are forced to endure multiple failed pregnancies and many dead babies. I am not sure how well elephants would hold up emotionally as mammoth factories.

And let’s not even go down the Neanderthal road! All these same issues would be there except we’d be dealing with near-human babies and women surrogates.

These sorts of things mean we need to really think about why we want mammoths, Neanderthals, Dodo birds or whatever. Are the benefits of resurrecting these species worth the risks to the individuals that need to carry them? And is it worth the suffering of all the individuals of that species who die an early, horrible death? There almost certainly needs to be a better reason than coolness to bring any of these animals back.

In fact, it may be best to wait until we can invent some sort of artificial womb. At least then we’d spare the pain and suffering of the surrogates.

TEDx DeExtinction

Foundation focused on bringing back species

Full version of the painting Gone.

Click here to see the key for all of these extinct species.

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.

Artist concept of exoplanet Gliese 667 Cc. Credit: L. Calcada/ESA

Welcome to Gliese 667 Cc. We hope you enjoy your vacation stay on this amazing planet. You have traveled 23 light years from Earth, but the wonders you will witness are well worth the trip.

It could happen, sometime in the future. Maybe. In the meantime, let's read the travel brochure.

Discovered long ago, in 2009, Gliese 667 Cc, as it was originally named, is a model of how un-Earth-like an Earth-like planet can be. First, you may notice that you've put on a few pounds under this super-Earth's greater gravity. You may also think you're losing your sight, since this planet's dim red dwarf sun shines only a fraction of the visible light Earth's Sun does. Finally, as promised, your vacation here will last an entire year and hopefully you read the fine print that this planet's year is only four weeks long.

Okay, back to reality. It's 2013, we do not (yet) have luxury cruisers warping people to other worlds, and we still haven't set foot on another planet. In fact, it's been less than two decades since we detected the first actual extrasolar planet (aka, exoplanet; planets orbiting stars other than our sun).

However, since that first exoplanet was found in 1992, we've made some decent progress in exploring other worlds out there, and may even be zeroing in on that "other Earth."

Today the count of confirmed exoplanets stands somewhere around 867, with another 2900 or so "candidates" whose existence is waiting to be confirmed. And over 2700 of those candidates were brought to our attention within the past three years by NASA's Kepler mission, whose goal is to find Earthlike planets—Earthlike, in terms of size and habitability potential.

In that mix are seven planets currently touted as potentially habitable—habitable to life as we know it, at least, with conditions that are friendly to the presence of liquid water. It should be noted that this is what scientists mean by habitability: conditions such that liquid water could exist, given an adequate atmosphere and an abundance of water molecules. This definition does not require that a human being could survive in that environment.

Back to Gliese 667 Cc. One of three exoplanets (two confirmed, one candidate) orbiting the red dwarf star Gliese 667 C (one of three stars in a triple star system), this one rates highly on the habitability scale (meaning we can imagine there being oceans, a water cycle, and potentially life), but at the same time is strikingly different in several ways to that prototype of Earthlike planets, Earth.

It is a "super-Earth", meaning, as you might expect, bigger than Earth: estimated at 4.8 times the mass of Earth. Depending on its diameter, that could mean surface gravity notably greater than what we're used to: things weigh more, rain falls faster, landscapes are sculpted with a heavier hand.

It orbits within its star's habitable zone—the proper distance so that water can be in liquid form—but since that star is a red dwarf, and much fainter than the Sun, that proper distance is much closer, about a tenth the Earth-Sun distance. Being so close to its star, Gliese 667 Cc only takes about 28 days to complete an orbit and mark its own year. Imagine a birthday party every month!

It has also been suggested that, since this super-Earth is so close to its star, it is probably tidally locked, rotating only once per revolution and keeping the same face toward its star at all times. This would give Gliese 667 Cc a "day" hemisphere and a "night" hemisphere, so you could choose the time of day you like and stick with it. It would also likely mean a perpetually hot side and a perpetually cold side—unless a thick, Venus-like atmosphere exists that might keep surface temperatures globally similar.

Between these extremes, in the twilight zone between day and night, perhaps would be a perpetually temperate ring bounded on one side by a cold dark vastness of hemi-global ice sheets and a vast realm of sweltering sauna lands and hot-tub oceans–something for every type of vacationer.

And one has to wonder what kind of weather patterns would develop on this schizoid super-Earth.

Such we can imagine. We don't know if Gliese 667 Cc has oceans, or what kind of an atmosphere—if any—it might possess. All we really know is its super-Earth status and location within its star's habitable zone.

Perhaps we'll learn other details in the future that will help us paint a more realistic picture of this exoplanet and get working on that travel brochure.

Fallen whale carcasses nurture a variety of deep-sea life from large crabs and fish to thick coats of bacteria. Photo courtesy neptunecanada of Flickr via Creative Commons

A new paper describes the slowly rotting skeleton of a whale on the seafloor near the South Sandwich Islands, between South America and Antarctica. Why is such a thing exciting to geologists? There are a couple of reasons.

When whales die, they drop dead wherever they happen to be. If they beach themselves first, their corpses lie on the beach, but most whales pass away at sea and sink. Once on the seafloor, their decomposing bodies, called "whale falls," amount to a winning lottery ticket for a host of creatures, which gather around the corpses and settle in to live off them. The flesh goes first, then come the fat-filled bones. The biological communities that arise may last for decades, perhaps centuries, depending on the local conditions.

Biologists are interested in whale falls as lovely self-contained examples of oceanic food chains. Geologists see whale falls as a rich study in taphonomy, their name for everything that happens to organisms as they become fossilized.

If you think about the exquisite fossils you see in museums, the marvel is how clean they are, as if a taxidermist had prepared them for burial. But nature is a lousy taxidermist. For every perfect museum skeleton there are drawers backstage stuffed with thousands of bony fragments, incomplete and imperfect in many ways. But what the fossil collector sees as lamentable damage, the paleontologist—specifically the taphonomist—sees as possible environmental data. Everything from the tooth marks of scavengers to the scrapes made by construction-site bulldozers is the kind of evidence that geology prizes for insight into the living world of the deep past.

Some of the first whale falls studied by scientists were found by the U.S. Navy while they were searching for something they'd dropped. Most whale-fall research, however, is done on carcasses that are towed away from beaches and deliberately placed on the seafloor. That kind of research is quite young, though, and to learn about the late stages of whale-fall existence we need natural examples that are older. It is way too expensive to just dive down and look around for them, so we have to grab the opportunities that arise while we're looking for other things.

The new paper was published in the journal Deep Sea Research Part II: Topical Studies in Oceanography in January (read it online). The British research ship James Cook was surveying a blown-out seafloor volcano full of hydrothermal vents (white smokers) when it spotted whale bones. The scientists alertly carried out a state-of-the-art study using the ship's underwater roving vehicle Isis, making a thorough video survey and grabbing some bone samples. It is only the sixth time that a natural whale fall has been examined in this much detail, and the first case from the Southern Ocean where whales are most abundant.

The paper is full of the kind of information that can be applied to fossils as we get our bearings in this field. The different stages of life on a whale fall leave different signs in the bones. The subject is complex, but that's what science is for. And the Bay Area's younger rocks, especially in the Santa Cruz area, are full of whale fossils. Modern whale falls can inform our understanding of the ancient times in which those whales lived and died around here.

Another thing that interests geologists, especially students of evolution, about whale falls is their role in the deep sea environment. Hospitable places in the deep sea are stepping stones for life, like oases in a desert or gas stations in Nevada. Many of the same species on whale falls also live on hydrothermal vents, which exist only in places where tectonic plates are spreading apart. Whale falls are scattered more randomly and allow the vent species to "island hop," keeping the seafloor a unified biome.

These matters are relevant to how Earth operates. The deep seafloor can be a source of new species when mass extinctions strike the surface world, and vice versa. How did this work before whales existed? Are there signs in the fossil record, or in the genetic records of living species, of this process at work in the past? Those are the scientific topics that this new set of whale bones will help us address.

New research explores the cognitive effects of listening to another person's cell phone conversation. (Photo by futurestreet via Flickr, CC by 2.0)

On a recent bus ride across the Bay Bridge, I was reading a journal article about environmental pollutants when a cell phone rang a few seats behind me, piercing the glorious silence. My muscles tensed, anticipating the inevitable banal chatter that I would have no choice but to endure.

“Hello?”

Pause.

“No, I’m not busy. I’m just on the bus.”

Long silence.

Then the person on the other end of the call must have launched into a seriously juicy tale, because the woman replied, “No!”

Long silence.

“I can’t believe he did that! Can you imagine?”

No, I can’t imagine. As I tried to contain my building frustration, after rereading a sentence five times with no hope of comprehension, I resolved to scan the scientific literature to find out why hearing someone talk on their cell phone is so maddening. But then more pressing matters got in the way and I forgot about it.

So I was interested when I heard about a new study published in PLOS ONE last week in which psychologists from the University of California, San Diego investigated this very question. Well, nearly so. Being cognitive neuroscientists, they weren’t measuring something as subjective as annoyance per se but more tractable scientific questions like memory and attention. And, yes, they found that hearing a one-sided conversation is extremely annoying and distracting—far more so than hearing both sides of a conversation.

Why study what’s become one of the most common examples of thoughtless behavior? Americans spent something like 2.3 trillion minutes on wireless devices last year, the researchers note in the paper, with some people confessing a “personal connection” with their cell. The sheer ubiquity of these insidious little devices means they will affect pretty much everyone at some point in some way.

Several studies show that chatting on cell phones while doing something else, like driving, interferes with your ability to perform that task—and you don’t improve with practice. The studies suggest that the effects aren’t related to motor skills, like dialing while steering, but to an inability to pay attention to what’s going on around you.

Walking while chatting isn’t much better. Like the famous gorilla-basketball study—where participants who watched teams pass a basketball back and forth failed to notice a person in a gorilla suit amble through—a 2010 study found that most pedestrians talking on cell phones failed to notice a clown ride past them on a unicycle. Cognitive neuroscientists call this phenomenon “inattentional blindness.”

If cell phones can compromise your ability to perform a task as ingrained as walking, it’s surprising that only 10 states prohibit drivers from talking on a handheld device.

It’s no secret that most people hate listening to others talking on their cell phone. Surveys support what we all assume, with more than 80% of respondents attesting to the irritation factor. But few investigators have devised experiments to understand the cognitive effects of listening to a one-sided conservation. So Victoria Galván, an associate professor of psychology at UC San Diego, set out to do just that.

To simulate what happens when we find ourselves hostage to someone jabbering on their phone on a bus or in a restaurant, Galván combined a well-controlled attention task experiment with a bit of deception. The study participants, 164 undergrads taking an Intro Psych class at the university, thought the study was about a link between anagrams and reading comprehension. (Fifteen of the students must have read the literature because they guessed the study’s aims, forcing the researchers to exclude their results.)

While the students worked on unscrambling anagrams, a researcher left the room. Then the conversations began: "confederates" sitting near the students started either one-sided or two-sided 7-minute conversations that covered details about a birthday party, shopping and a date. When the researcher returned, she said her team wanted to understand “how a conversation affected a person” and gave the students a test to measure their memory of the conversation and a questionnaire to assess how distracting it was.

As predicted, the students who heard the one-sided conversation were more distracted and had more trouble with their anagrams. They also found the volume and content of the conversation more annoying. Sound familiar?

The researchers attribute our annoyance in part to a lack of control, which other studies show can lead to heightened stress responses such as headaches and anxiety.

Interestingly, the students who heard the one-sided conversations performed better on the memory task, a result that may relate to the “unique, intrusive, ‘attention-grabbing’ aspects of a one-sided cell phone conversation," the researchers explain, since the students weren’t instructed to pay attention to the conversation. Or maybe they remembered more because they had half the information to absorb.

I’m betting on the unique, intrusive, attention-grabbing hypothesis. A previous study in a lab setting by a different research team suggested it’s the unpredictability of one-sided conversations that gets under your skin. When you hear two people talking, you don’t waste cognitive resources trying to guess what the other person is saying and it’s easier to block them out. (And I might have learned what that no-good guy did.)

But when you can hear just one side, you’re left waiting for the next snippet, imagining what comes next. I certainly had to use a lot of brain power to stay focused on that journal article, which I could finally read in earnest only after my fellow passenger ended her call after 15 very long minutes. Luckily, she did it before I gave her something else to talk about.

Brandt's cormorants. Image courtesy of the National Park Service.

Last March, one of our QUEST contributors, Thibault Worth, wrote a piece about the fluorescent millipedes that were unexpectedly discovered on Alcatraz during a survey of the rat population on the island. As we were eager to learn more about these fascinating arthropods, I and my several of my KQED Science colleagues headed to Alcatraz with forensic entomologist Dr. Robert Kimsey, the National Park Service's Integrated Pest Manager Bruce Badzik and the UC Davis Entomology Club.

This was my first visit to Alcatraz, and my general impression of the island was as Badzik described it to me during our interview: “Most people are fascinated with the history of the federal penitentiary on Alcatraz because of the well-known criminals such as Al Capone, “Creepy” Karpis, the “Birdman of Alcatraz” and Machine Gun Kelly. There were also a lot of movies made about Alcatraz: Murder In The First, The Rock, Escape From Alcatraz with Clint Eastwood. So people love to come out to see where those films were filmed and see what they can see of it.”

I didn’t realize it also has a thriving water bird population and serves as a sanctuary to a diverse number of species.

“Folks who may not be interested in the prison love to come out here and see the large quantities of birds that we have that inhabit the island, such as the pelicans, the Brandt’s cormorants, the black-crowned night herons, the snowy white egret, mallards and a whole host of other sea birds that call this place home,” says Badzik.

Senior Interactive Producer Craig Rosa and Multimedia Producer Joshua Cassidy served as camera and sound on the millipedes shoot.

And the name of the island is derived from the Spanish word, "alcatraces", another indicator of its avian history.

“Other people talk about it meaning strange white bird, but Alcatraz basically means pelican,” says Badzik. “This island, before it became a federal institution, was just covered with pelicans. Folks talked about how this was just covered in guano. Some folks actually called this 'White Island', just because of all the guano out here.”

Dr. Kimsey adds, “When the National Park Service got the island assigned to them, water bird rookeries began to develop and so now for a large part of the year, a large fraction of the island is closed because these rookeries are protected by federal law. And so the ecology of the island [over time] has changed rather considerably.”

Unfortunately, I didn't have time to get a tour of Alcatraz while we were there, so I'll have to go back to check out the penitentiary. But it was a real privilege to be able to gain access to the more restricted portions of the island. We filmed our interviews in one of the private gardens created by its previous military residents.

As we shot most of our footage at night, filming in the darkness posed some technical challenges for the crew and evolved into a "hunting-the-hunter-with-lights" scenario.

Multimedia Producer Joshua Cassidy films Alex Nguyen looking for milipedes on Alcatraz.

Alex Nguyen, the UC Davis undergraduate student who originally found the millipedes last winter, would shine his UV flashlight on the ground in search of millipedes and we'd closely track him with a high-powered portable LED light. When he finally found his first millipede, we were just as enthralled as he was when it glowed a brilliant turquoise blue under the UV light.

Want to learn a few more basic facts about millipedes? Check out this Popcorn Maker-enhanced web extra featuring Dr. Kimsey.

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.