Mushrooms are the main attraction all weekend long at the Santa Cruz Fungus Fair (photo: E. Loury)

Erin Loury

by Erin Loury

After four years of living near Santa Cruz, last weekend I finally ventured to the annual Fungus Fair for the first time.  With elements of nature, science, and hippie culture, it’s an event that sounded just so… Santa Cruz.

My expectations were tempered after hearing Meghan’s first radio story for KUSP, which shadowed volunteers searching for mushrooms to display.  The weather has been so unusually dry this winter that fresh fungi seemed to be in short supply.  In fact, I overheard a fair organizer say that this was the first year they had to send mushroom collectors out of the area, in search of wetter conditions farther north.

So while I was expecting maybe a few tables with mushrooms on display, I was startled to enter the Louden Nelson community center to behold – trees.  They had recreated a little piece of forest with artfully arranged fungi springing out of the logs and redwood duff.  And the tables were loaded with mushrooms galore.

The fair is an opportunity for a little indoor mushroom foraging. (photo: E. Loury)

The diversity of local mushrooms stunned me, especially their shapes and colors.  I enjoyed hearing mycologists, such as Chritstian Shwarz, leader of the UCSC Mushroom Enthusiast club, speak about their study subjects with the same level of enthusiasm I’m used to hearing from my former marine scientist labmates when they talk about the ocean.

My main draw to the fair was a talk about sudden oak death by David Rust, co-founder of the Bay Area Mycological Society.  This quarter I’ll be learning the ins and outs of the disease as part of my feature story for Science Notes, and I was intrigued by how the disease affects not just the mighty oaks, but all the species connected to them.  Many mushrooms grow on oak trunks and roots, and some are species-specific.

A small sampling of the diversity on display (photo: E. Loury)

Rust’s talk was a great primer in the history and basics of the disease. I learned that the pathogen – a fungal-like organism related to potato blight – hitchhiked into California on ornamental nursery plants from Europe.  While the disease only causes cosmetic damage on the leaves of camellias and rhododendrons, it took a lethal turn once it spread to some of California’s native trees. Rust explained how the California bay laurel serves as a host for the disease’s multi-stage life cycle, and that the tanoak, while not a true oak species, is most susceptible to the disease.

Rust urged mushroom hunters to use caution when collecting – the pathogen can be spread by clinging to the wet mud on a hiker’s boots.  The audience uttered some groans of disappointment and dismay as Rust flashed photos of half a dozen fungal species associated only with tanoak trees – species they are in danger of losing if tanoaks disappear.

A cauliflower mushroom - my personal favorite! (photo: E. Loury)

I left the talk with my head buzzing with avenues of inquiry to explore for my story, and visited the rooms of vendors selling everything from mushrooms you could grow yourself, to beautiful fungal-inspired artwork.  I couldn’t help but buy a pair of mushroom-printed socks.  I rounded off my visit by sampling the mushroom quiche, and bringing my camera to the identification table to ask about a photo I had taken of a fungus among the redwoods on the UC Santa Cruz Campus. Most likely a conch, I was told, a hard and woody mushroom that grows on the sides of trees.

Next week Christian Schwarz has agreed to take me tramping around the UC Santa Cruz campus to check in on some of the oak trees and their mushroom tenants.  I look forward to sharing what I find!

A charismatic mega-fungus (photo: E. Loury)

A new type of reporting? Photo by Meghan Rosen

By Meghan Rosen

David Cohn doesn’t look like the new face of journalism.  He’s boyish, with an untamed mop of black curls and a stubbly beard: Picture a darker Mark Zuckerberg, but more stylishly dressed.

It’s early in the morning when Cohn comes to talk with our class about Spot.Us, his three-year-old experiment in crowdfunding journalism, but he thrums with energy. If I had to pick one word to describe Cohn, I’d say ‘caffeinated.’ Or ‘bright-eyed.’ Or maybe even ‘feverish.’  You get the idea. Cohn’s passionate about his experiment, and it shows.

I’d heard of crowdsourcing before (Wikipedia), and even crowdfunding (my husband and I registered at the microlending site Kiva.org for our wedding), but crowdfunding journalism was a new idea for me.  It probably shouldn’t have been; Cohn’s website, Spot.Us has been matching freelance reporters with funding for three years.

But he’s the first to admit that he didn’t invent the concept of donating to journalism: People have been contributing to NPR for decades.  The difference is the level of transparency.

“When you donate to NPR,” he said, “You cover your eyes, throw money over a fence, and hope that it goes towards good journalism.”

With his organization, donors don’t have to trust that their money is being used for good; they see exactly where it goes.

So, how does Spot.Us work, exactly? Reporters come to the site and pitch an idea for a story. They estimate the cost of reporting (travel, freelance writing rates, etc), and then, they wait for people to donate.

“They’re pitching to the world,” Cohn said, “And the world collectively has a freelance budget.”

Potential donors peruse a ‘menu’ of story ideas, and contribute to those they’d like to see fleshed out and reported.  People can choose which news to support, and they can donate just a few bucks. (Reporters can pitch anything they’d like to write about, but Cohn weeds out certain types of stories. Breaking news, for example, doesn’t work because Spot.Us reporters have to wait for funds.)

Most of the money Spot.Us raises comes from small donors, though the largest donation they’ve received came from Barbra Streisand, for a story about the Great Pacific Garbage Patch.

“My mother was thrilled,” Cohn said.

60-65% of pitches get funded, and Spot.Us typically publishes two to three stories per week. Spot.Us isn’t going to sustain a freelance career, Cohn said, but it can be part of multiple revenue streams for a reporter.

“It’s just another thing for reporters to have in their toolkit,” he said.

Cohn talked with our class for more than an hour about the changing world of journalism, and how to use the Internet as a testing-ground for new ideas. How does a 29-year-old writer (he started out as a tech reporter for Wired, then worked at Seed Magazine) conceive of and market a radical concept like Spot.Us?  What can beginner journalists like us learn from this self-proclaimed ‘geek reporter’? I wanted to know more.

So, I interviewed him.  Here’s what he had to say.

20 minutes with David Cohn

How did you spread the word about Spot.Us in the beginning?

Well, first of all, I was a relentless self-marketer. And, I was lucky that I had some kind of connections and media relations already.

I also blogged about it.  At the time we launched Spot.Us, the concept of community-funded reporting was weird. So, I created this narrative: ‘Hey guys we’re trying a crazy experiment, and I invite you to follow along.’

I’m a big evangelizer in terms of experimentation. One general rule of the Internet is that it’s cheaper and easier to try something than to debate whether or not to try it.

People were watching what we were doing not just to see what happened with Spot.Us, but for this meta-narrative.

Do you think it’s important for journalists to use social media like Twitter and Facebook?

I wouldn’t get caught up in the ‘Twitterness’ of Twitter. It’s just a new way for people to communicate.

Do you tweet?

I do tweet. I am a tweeter. I jumped on it relatively early- in 2007. In the beginning I followed everybody, but now I follow around 2000 people.

How many people follow you?

10,000.

[David Cohn’s twitter handle is Digidave. As of Dec. 5, he had 10,381 followers, including me.]

After Twitter, what’s the next new thing in social media?

Twitter is not going away. The company might die, or change, or a better product might come along, but the vocabulary isn’t going to change. So, even if you spend a lot of time on Twitter, your time isn’t going to be wasted, because you will learn from it.

What topics did you initially think Spot.Us would cover?

When I first launched Spot.Us I was in San Francisco, so I had on San Francisco blinders. But I instantly started getting stories about the Oakland police.  So, we’ve done a bunch of Oakland police stuff, but there are all these other issues in Oakland that just don’t get covered- like crime spotting, neighborhood associations, and certain PTAs.  They are serious issues. The Chronicle doesn’t cover them, and neither does the Tribune.

Things are bubbling up even more lately, with the Occupy Oakland stuff.  We’ve raised $2000 to help reporters cover it.

Now that Spot.Us has spread beyond San Francisco, what’s next?

Spot.Us will continue growing. But we have big news — We’re becoming a partner with the longtime nonprofit organization, American Public Media.

It’s an acquisition, though, not a buyout. I’m not going to be a millionaire.

[David says he’s a shameless self-promoter, but when he talked with me about the APM partnership, he was really very humble. He didn’t, for example, tell me that APM is the largest owner of public radio stations in the country, or that after NPR, it’s the second largest producer of public radio.  But I didn’t have to know those things to understand that the news was A Big Deal.  David’s excitement was palpable. He made me promise not to spill until APM announced the acquisition publicly, which they did just six days ago, on Nov. 29.]

Congratulations! What does that mean for you and Spot.Us?

Spot.Us was just me and one other person, and I wanted to see if we could make it grow. As an experiment, I consider it a success. Now, it needs to become part of a larger organization.

I’m still going to be there, but technically, I’ll be ceding control. I’m excited to pass off some of the business duties. I don’t want to cut any more checks!

Are you working on any new projects?

I have a few babies in the idea phase. Some wouldn’t require that much time, but I’ve just never taken the time to get them started.

Daniela Hernandez

By Daniela Hernandez (Twitter: @danielaphd)

Neuroscience, physics, biology and birds are recurring topics of my conversations with Dennis Taylor, the community conversations editor at The Salinas Californian, where I interned during fall quarter.

Western bluebird perched on bare branch. Photo Credit: Wikimedia Commons

Every time I speak with Dennis about anything remotely scientific, a look of genuine excitement and interest comes over him. During one of our chats, he told me about the work he does with the National Audubon Society as a citizen scientist in Gilroy, California.

Here is a brief Q&A about his work. It has been edited for clarity:

What inspired you to volunteer at the Audubon Society?

I have always stayed abreast of developments in threatened species – what are the pressures reducing their numbers? And overwhelmingly the greatest pressure is habitat loss. I stumbled into the Audubon Society because I wrote a story about an older gent who I would walk with as he would check “bird houses” constructed by the Audubon Society that were hung in trees or perched atop poles in open grasslands. Norm was his name, and what we were doing was providing habitat that was lost to sprawling home construction.  He had several miles of trails with over 100 houses he would need to check weekly. He died about a year after we began working together and Audubon came to me because no one knew the species and the trails like I did.

What kind of work have you done for them?

I begin in early spring by checking all the houses to get rid of roosting waste from the winter and make sure there are no wasp or yellow jacket nests built inside the houses. Then I walk and watch. Within a couple of weeks I begin to see mating flights, flirtatious mid-air dances. Within another week or two, I begin to see the birds carrying debris for their nests. (Different species use different materials for their nests; some use straw, others use twigs.)

When I don’t see the mother out flying, I carefully lift open a special door to the box and feel for eggs gently with one finger. I record the number of eggs in each of the 100 houses. After another week or two, there’s usually a furry head: the chicks. I compare the number of chicks hatched to the number of eggs and note the mortality rate. Then I walk and watch some more, and when I see little heads sticking out I know they are about to fledge, so I count the fledglings and compare that number with the number of chicks to see if there were additional deaths.

I collect that data onto a spreadsheet and transfer it to a database at Cornell University, which tracks bird populations all over the country. So when you read a story about “Western Bluebirds in Decline,” that’s how they know. The program used to be called the Bluebird Recovery Project, but about three years ago it was changed to the Cavity Nesting Project, to more accurately reflect what we do.

Western Bluebird Sialia. Photo Credit: Wikimedia Commons

We track all species of birds that must nest in hollows of trees. In my region this includes western bluebirds, tree swallows, chestnut-backed chickadees and white-breasted nuthatches. When you cut a tree to build a house in an oak forest, you eliminate habitat for these particular birds.

You mentioned you worked with kids. What do you teach them during the field trips?

My teaching is geared to the age of the children that come with me on a particular field trip. “Certain birds will only have babies in holes of trees,” for the youngest. Or, “The way certain species protect themselves is by entering a cavity in a tree that is only millimeters wider than they are, protecting them from larger predators like other birds, raccoons and even snakes,” for the older kids.

I take the kids on one of my shorter walks during which I usually pull down a house [so they can see the birds]. I usually wait until the chicks are about to fledge but can’t quite fly yet. This reduces the chance of injury to the fledglings [and the kids!]. I point out characteristics such as yellow bands that often appear on the inside of the beaks of the fledglings that help the moma bird zero in on the little mouths when they are dropping food such as insects.

Sometimes I will gently reach in the nest and pull out a fledgling and let the kids gently stroke its head. One time I was doing that, and as I was feeling down in the nest I found a dead chick. I need to remove dead chicks straight away because as they decompose it creates opportunistic bacterial infections for the other chicks whose immune system isn’t fully developed. So I hid dead chick back in my palm, covering it with a couple of fingers, while pulling the live one out with my thumb and index finger. [The kids] were never the wiser.

Western Bluebird using Nest Box. Brood unknown. Photo Credit: Wikimedia Commons

And then there was The Day of the Blue Jay. One nest had fledglings that could actually fly a little ways, to my surprise. Three bolted out of the nest and a cacophony of screams followed three skirting chestnut-backed chickadee fledglings down the path we were on. I caught one, and my assistant caught another. As I turned to go after the third, a blue blur whizzed by a few feet to my right, down the slope on the side of the trail. Of course I had 20 pairs of little eyes following the jay as he swooped down on the fledgling and … poof! …. Little brown feathers exploded into the air. Little heads slowly turned to me, mouths agape. “Well,” I said, “Blue jay chicks need to eat too.”

As the kids were walking back down the trail, my partner turns to me and says, “Blue jay chicks need to eat too? That’s the best line you could come up with?”  And we begin laughing. So I’m sure in the kids’ minds Mr. Birdman was not only a chickadee chick killer, he’s a sinister one that laughs about it.

Then of course I tell the kids that if we keep cutting down trees the babies you are looking at will have no place to live.

Why do you volunteer?

It’s cathartic for me. We tend to view biology in compartmentalized frames – birds in this sector, canines over there, and humans in this square. We don’t live in a vacuum, and the sooner we realize that the better off we and other living things will be. Author John Muir (and my grandmother, less eloquently) said “that when we try to pick anything out by itself, we find it hitched to everything else in the universe.”

[The work is] also immensely interesting. The longer I do it, the more science I learn – migratory patterns, food variables, acute avian viruses (because of West Nile I’ve taken to wearing masks and latex gloves when opening the houses, but I draw a smiley face on the mask – hey, it works for human babies), seasonal nesting variations, anomalies in any of these, and on and on.

Is there anything else you want to tell me?

Programs like this are critical to supplementing children’s science educations. With standardized testing, the lion’s share of effort is being spent on math and language arts. Sacrificed are the sciences and humanities. The broader science community needs to step up and help get children excited about science – no better place than in the field.

Follow Dennis Taylor (@scribedenny) on Twitter.

You can read more about his work in an article by the Gilroy Dispatch.

The latest information to suffer this fate is from a story about Tamara Patton, a graduate student at the Monterey Institute for International Studies, who’s 3d modeling nuclear processing facilities using self-devised methods.

Nuclear Programs Worldwide As of 2005 (Red means a "Nuclear Weapon State" by the Nuclear Non-proliferation Treaty, Orange are other nuclear powers, Yellow are countries suspected of having nuclear weapons or programs, Pink are countries known to at one time have a nuclear weapon or a program. Courtesy of Wikimedia Commons.)

Now, modeling nuclear sites in 3d is not new, she told me. But apparently it is usually used by organizations like the International Atomic Energy Agency to determine where to place surveillance cameras and to plan inspections ahead of time, so they can optimally use the limited time they do have while physically on-site. With a virtual avatar, they can walk around a virtual building, like second-life or a videogame.

What is unusual is that she’s done this all using publicly available tools and resources. Google SketchUp provides the interface to push and pull shapes around to make three dimensional objects. Google Earth provides satellite images that she uses as the templates for her models. Though the overhead view by Google Earth doesn’t provide as much detail as close-up, on-site photography, Patton analyzes the shadows from the limited photographs combines them with time of day and location to accurately determine height.

She’s used her techniques to provide evidence that a textile factory is really just a textile factory and to help determine the production capacity for a nuclear facility of Pakistan.

It’s part of a new wave of intelligence where citizens without access to special tools or restricted information can participate, said Assistant Secretary of State Rose Gottemoeller of the Bureau of Arms Control, Verification and Compliance, in a speech at Stanford on Oct. 27 titled “Arms Control in the Information Age.”

There she asked:

Can we incorporate open source information technologies and social networking into arms control verification and monitoring?

What does she mean by this? She thinks that large groups of people can work together to either generate new sources of information gathering of dangerous weapons or provide deeper analysis of existing information.

Looking for nuclear materials in the digital age (Courtesy of Wikimedia Commons)

For information gathering, she cites the Defense Advanced Research Projects Agency Red Balloon challenge as an example, where the agency offered a $40,000 reward to the first team to find 10 identifiable red weather balloons moored throughout the country (Out of 4,300 teams, an MIT team won in under 9 hours).

Then she extrapolates it to arms control:

Now, how could something like this work in an arms control context? Let’s just imagine that a country, to establish its bona fides in a deep nuclear reduction environment, may wish to open itself to a verification challenge. It could seek to prove it was not stashing extra missiles in the woods, for example, or a fissile material production reactor in the desert.

Of course, it sounds like there are a lot of potential holes in the challenge– blocking access, intimidating participants, fabricating results, plus the entire idea of offering an incentive not to find something– but she invited the audience, future members of the intelligence community, to come up with solutions.

The other half of her proposal was to use open source solutions to analyze publicly available information. In addition to Patton’s work, Gottemoeller cited the work of Laila Shereen Sakr, who predicted the fall of Libyan towns and cities hours beforehand, by building software that analyzed tweets from twitter and finding trends in hashtags.

It’s a far different way to do intelligence.

Sarah Jane Keller

by Sarah Jane Keller

I grew up near a fortress built during the French and Indian War and used to love historical reenacting, but I eventually quit. In the eyes of dominant reenacting culture, period-correct portrayal of a frontier woman meant that my male friends would be throwing tomahawks and shooting muzzleloaders, and I’d be mending bodices and cooking over an open fire.

The next time you inhale too much smoke while roasting marshmallows, ask yourself what it would be like to have that crud in your lungs every day. (Photo by SJK)

While I had the luxury of eschewing the cooking technology of the colonial period, almost half of world’s families still prepare their meals over open flame. And just as in early America, men are often out and about, while women and young children stay in the home where they continually inhale smoke.

This October, a Science paper from authors at the National Institutes of Health (NIH) named home pollution from open cooking fires the world’s leading cause of environmental death. Killing nearly 2 million people annually, indoor air pollution is more deadly than malaria, according to the World Health Organization. Most of the deaths come from acute lower respiratory infections in children under five and adult deaths from chronic obstructive pulmonary disease, which includes chronic bronchitis and emphysema.

I’ve recently become more aware of this issue because I’m writing a story about the Berkeley-based Darfur Stoves Project. Just after I started talking to people involved with the Darfur Stoves Project, I interviewed Bill Toone, the executive director of the San Diego-based ECOLIFE Foundation, about monarch butterflies. Both organizations distribute fuel-efficient cooking stoves in ways that are culturally specific, address the extreme logistical challenges of distributing a new technologies in poor countries, and attempt to create market demand for the stoves. The NIH authors list all of those things as barriers to stove adoption by families.

Monarch butteflies hang from a tree for winter warmth in Mexico. Photo by: Ernest H. Williams

These projects demonstrate how food—and its preparation—directly touch individual quality of life, but then ripple into our local environments and, in the case of carbon emissions, the global environment.

As Toone said: “This is one of those wonderful crossover spots where we can help the environment, help a family and help ourselves in the sense that these cooking practices have an impact on our climate.

Since 2004, Toone and ECOLIFE have been working with communities in and near Central Mexico’s Monarch Butterfly Biosphere Reserve to distribute fuel-efficient cooking stoves. Deforestation over the decades–both by illegal logging cartels and locals, who need firewood for cooking—has fragmented the butterflies’ unique Oyamel fir habitat and put the migration at risk. ECOLIFE recognized that communities could reduce pressure on the habitat that they share with the butterfly by using less firewood to prepare their meals.

Toone’s approach to biological conservation comes from his conviction that people need to have adequate food, water and shelter before they can care for other things. “The most effective way we’re going to enact conservation on the planet, is that conservation is how we ensure our healthy survival into the future,” said Toone. “It’s really about us.”

When ECOLIFE tried to save money by removing the tile indicating that the Lorena cookstove is a friend of the butterflies, new stove users wondered what happened to the tile, and ECOLIFE restored the important symbol of the community's connection to the environment. Photo credit: ECOLIFE Foundation

The Darfur Stoves Project is another stoves group working for human and environmental health. In 2006, the U.S. Agency for International Development approached Ashok Gadgil, a

The Berkeley-Darfur Stove is manufactured in Mumbai, assembled in Darfur, and was designed in tested by Lawrence-Berkeley labs engineers with constant input from the women of Darfur. Photo credit: LBNL Cookstoves Project

physicist at Lawrence Berkeley National Laboratories, to help because militiamen were raping Darfuri women as they left refugee camps to search for firewood. A fuel-efficient stove would cut down on wood-gathering trips and women’s exposure to violence.

The stove that Gadgil and his team developed is the product of a long, iterative process between engineering and culture. The stove has been successful because it incorporated many design suggestions from Darfuri women. Now that there are few trees left to gather around the refugee camps, many women buy firewood rather than collect it, and the stove saves them money and time.

Andree Sosler, the executive director of the Darfur Stoves Project, told me in an interview that will appear elsewhere, about their most recent work in marketing the stoves and providing microloans so that women may purchase them. Like the NIH paper, she emphasized the importance of developing a market for stoves because it helps make the product more consumer-driven and sustains its distribution.

Though Toone is a conservation biologist who once worked on the California condor reintroduction, and Ashok Gadgil is a physicist and engineer, I heard a similar refrain from both of them. They weren’t satisfied with just working with animals or making gadgets, they wanted to see real changes in the quality of life of individuals.

Gadgil, a master of developing technology for people who are often overlooked by traditional research and development, summed up his motivations in an interview earlier this fall: “How can we say at the end of the day we made the world a little better. Do you say: ‘I want to publish one more paper’? No!”

Beth Marie Mole

By Beth Marie Mole

Did you remember to invite your relatives to Thanksgiving?

How about your extremely distant relatives?

Lemur Feast. Courtesy of the San Francisco Zoo

The folks at the San Francisco Zoo remembered. In fact, they laid out their fine china, cooked a colorful feast, and pulled up chairs for 15 distant relatives—the zoo’s lemurs.

In an event called ‘Feast for the Beasts,’ the zoo’s adorable primitive primates enjoyed a banner Thanksgiving banquet. The menu included green beans, fruit salad, sweet potatoes, and a faux turkey made from monkey chow. Guests drank from champagne glasses filled with apple juice and adorned with grapes. No word on whether they made a toast, though.

The party started in proper seats, according to zoo official Lora LaMarca. But the lively lemurs quickly threw the ‘elbow rule’ aside—along with general etiquette—as they hopped onto the table to enjoy their good eats.

Keep your tail off the table! A lemur enjoys some fruit while committing a feast faux pas. Photo courtesy of Susan Schafer

The Thanksgiving feast isn’t just a special treat for them, though; it’s also an exercise. Zookeepers wrapped some of the food in little boxes, providing a playful search that employs the foraging skills they would rely on in the wild.

The fifteen lemurs—6 ring-tailed, 4 red-ruffed, 3 black and white, and 2 black—live and monkey-around in the zoo’s lemur forest, which was founded in collaboration with the Madagascar Fauna Group. The group works on conservation efforts in the lemur’s homeland of Madagascar where they face deforestation, hunting, and illegal pet traders.

A red-ruffed lemur enjoying some juice. Photo courtesy of Susan Schafer

Madagascar, which is roughly the size of Texas, hosts 5% of the world’s plant and animal species.  There are approximately 100 species of lemurs there—depending on how you define species—and they’re all considered either endangered or threatened.

Madagascar is located off the eastern coast of Africa and is the world's fourth largest island. Photo by Beth Mole

But in San Francisco, the only thing they’re in danger of is having bad table manners.

Happy Thanksgiving!

Helen Shen

by Helen Shen

I didn’t grow up eating Thanksgiving dinner, but over the years I’ve learned how to do the traditional American turkey-day right. There’s the carving of large birds, the mashing of potatoes, and of course, the skipping of lunch.

Most people I know skip lunch on Thanksgiving. We may call it “saving room for dinner,” but aren’t we really just buying caloric credits for the inevitable metabolic assault? This year, I wanted to explore the scientific evidence that either supports or debunks this holiday eating strategy.

Unfortunately, PubMed has exactly zero hits for the search term “Thanksgiving lunch.” Researchers I contacted directly or through news officers at Stanford University and UC San Francisco did not feel up to speaking on the subject of how meal timing (or skipping Thanksgiving lunch) affects metabolism.

Lunch — the other Thanksgiving meal. (Photo by Helen Shen)

I can imagine why some scientists might not want to touch this question with a ten-foot pole. With the Centers for Disease Control and Prevention reporting that 33.8% of American adults are obese, everyone just wants to know the simple bottom line on what we should eat, how much, and when. But biologically speaking, the human body may not lend itself to a straightforward answer.

Here’s an example. You may have heard some reports that eating breakfast could help you lose weight, while skipping breakfast could lead to weight gain.*

But consider this paper, published in The American Journal of Clinical Nutrition, in which 52 obese women, some of whom were habitual breakfast eaters and others breakfast skippers, were randomly assigned to eat or skip breakfast every day for 12 weeks. The two groups (eat versus skip breakfast) were given different sample menus to follow for the rest of the day that were matched in total calories and nutritional factors.

The confusing result: baseline breakfast eaters lost weight when they skipped breakfast every day, while baseline breakfast skippers lost weight when they ate breakfast regularly.**

What???

Obviously, it’s complicated. And as a scientist, getting large numbers of people of similar genetic makeup, with similar exercising, sleeping, and smoking habits to eat exactly what and when you tell them is also… complicated.

But getting back to skipping Thanksgiving lunch… The most interesting research paper I found, and the one most relevant to my original question, comes from the niche field of studying Muslims fasting for Ramadan.

In a study published online Nov. 13 in the Journal of Public Health, British researchers studied weight change in observant Muslims during and after the month-long Ramadan fasting period. Between Aug. 11 and Sept. 9, 2010, the 202 study subjects did not eat or drink between sunrise and sunset.

The participants, primarily male worshipers at the East London Mosque, were weighed at the beginning and end of Ramadan, as well as one month later. In all, 62 percent of participants lost at least 0.5 kg (1.1 lbs), 17 percent gained at least 0.5 kg, and 21 percent did not change their weight appreciably.

I like this study for a few different reasons. First, like the above breakfast-skipping paper, the study employs a per-person, intervention-style design, looking at the very same people before and after a change in daily meal schedule (and controlling for some of the genetic and environmental differences that plague many population-level studies in this field).

But, importantly, unlike the breakfast-skipping study, participants were not selected for being obese. Thus, the Ramadan fasters were less likely than the obese breakfast-skippers to be trying other, non-study-related strategies to lose weight during the observation period (which fall into the category of terribly uncontrolled factors***).

Lastly, as the authors point out, because the Ramadan fasters were not skipping meals to lose weight, they might be more likely to indulge in a large meal at the end of each day’s fast. So, this paper may be the closest we can come to studying what happens when we skip Thanksgiving lunch to feast at dinnertime.

I’m inclined to believe that if the Ramadan fasters skipped breakfast and lunch for a whole month, potentially binged on late dinners, and did not gain massive amounts of weight (and even lost weight in many cases), we’re probably all OK skipping lunch just on Thursday. Any conclusions beyond that are just gravy.

References:

Schlundt DG, Hill JO, Sbrocco T, Pope-Cordle J, Sharp T. The role of breakfast in the treatment of obesity: a randomized clinical trial. Am J Clin Nutr. 1992 Mar;55(3):645-51.

Hajek P, Myers K, Dhanji AR, West O, McRobbie H. Weight change during and after Ramadan fasting. J Public Health (Oxf). 2011 Nov 13. [Epub ahead of print]

* WebMD cites this paper, which finds children who regularly eat breakfast tend to have higher metabolisms. (Research funded partly by the Florida Department of Citrus.)

** Interestingly, the authors conclude by recommending that people who normally skip breakfast and are hoping to lose weight should be encouraged to start eating it regularly. In contrast, they balk at recommending that regular breakfast eaters who lost weight by skipping breakfast should keep up the new habit (“Although subjects who initially ate breakfast lost more weight in the no-breakfast group, we do not believe that these individuals should be advised to stop eating breakfast…”)

*** Could it be that all the obese subjects wanted to lose weight, and those who implemented one lifestyle change (switching their breakfast habits, whether eating or skipping), were more inspired to make other changes to lose weight?

Rows of native plants at the Thimann Lab greenhouse, grown for coastal prairie restoration (photo: E. Loury)

by Erin Loury

There’s a room at UC Santa Cruz filled with chocolate and vanilla, cinnamon and green tea, bananas and pineapple.  But far from ready-to-eat desserts, all are leafy and green, basking in the humid light of one of the three UCSC campus greenhouses.

A certain former UCSC student and plant aficionado in my life recently told me about the greenhouse on the roof of the Thimann Lab building.  Anyone can pop up to this greenhouse on weekdays from 9 a.m. to 3 p.m., and I came across some students studying at tables on the plant-covered patio.   The oldest of the campus greenhouses, it’s primarily used for instruction.

Workspace in the Thimann Lab greenhouse (photo: E. Loury)

Plant lab sections can visit a room full of carnivorous plants (I should have asked if they have this one with peculiar diet preferences), and also a tropical plant collection, which boasts the disproportionate number of tasties I mentioned earlier. There’s even an outdoor classroom up here, complete with speakers and a whiteboard.  If only all students were so lucky!

Jim Velzy, UCSC greenhouse director, points out two different species of plants in a hybridization experiment - brought back memories of Punnett squares! (photo: E. Loury)

Jim Velzy, the greenhouses director, was kind enough to give me a tour of all three greenhouses, including the ones used for research atop the Sinsheimer Labs and the Interdisciplinary Sciences Building, which are not open to the public.  All the greenhouses are located within a stone’s throw of each other, which is probably a good thing since it’s just Jim, the greenhouse operation’s manager Denise Polk, and four student employees that care for all the plants.

Some of the plants grown on the Thimann lab building, Jim told me, are for a coastal prairie restoration project near the Seymour Marine Discovery Center at the campus’s Long Marine Lab.  Seeds collected from native plants sprout in dozens of plastic tubes, awaiting transportation to the field.

Two campus divisions, Physical & Biological Sciences and Social Sciences, share the funding of the greenhouses, and researchers have free access to pots, soil and space. They can reserve a greenhouse and tailor it to their specific needs, like one that is currently sealed up and pumped with elevated levels of carbon dioxide.  Jim estimates that about 25 different projects occupy his 10 growth chambers, 10 incubators and 15 greenhouses at any given time.

“This facility is unique in that the instructional facility and the research facility are the same unit,” Jim said. “That’s not the case almost anywhere you go.”

Undergraduate students benefit from access to the state-of-the-art greenhouses, and a direct connection to ongoing research.  Students can work with the greenhouses for a senior thesis or volunteer with research projects.  Researchers benefit from the extra labor counting seeds or planting plants, and the connection to the instructional greenhouse gives them some overflow space for their experiments.

“Our biology faculty generally look at populations, distribution of species, speciation,” Jim said. “Those are all our claims to fame.”

On our tour, he showed me several experiments involving the hybridization of two closely related species.  A student in Dr. Kathleen Kay’s lab is studying how two species of goldfields that are nearly identical, and often grow next each other, maintain their distinct identities.

He also showed me endangered California wallflowers native to sand hills grown by Dr. Ingrid Parker’s Lab, and an experiment investigating how invasive Scotch broom suppresses the growth of Douglas fir seedlings.

A growth chamber maintains constant conditions for a flat of woodland stars. (photo: E. Loury)

We poked our heads inside growth chambers used by Dr. John Thompson’s lab.  Jim called Thompson a “father of coevolution,” the study of how closely connected species, like plants and pollinators, change together over time.  Jim showed me Lithophragma, or woodland stars, that have coevolved with a species of moth that lays its eggs inside the flower, and also pollinates the flower.

Another greenhouse overflowed with spiral ginger plants from Costa Rica, which have coevolved with hummingbirds, as seen in their flowers with a distinctly hummingbird-tailored, sippy-cup-like extension.

Sprial ginger flowers have evolved a perfect fit for their hummingbird pollinators (phto: E. Loury)

Achieving constant, reliable conditions in incubators (which are used to germinate plants), and growth chambers (which maintain constant light and humidity) are key to producing publishable results, Jim said.

“When you publish a paper in Science, Nature, Plant Physiology, whatever you want to publish in, the better publications are going to require that you have your plants under set conditions,” Jim said. “You eliminate all variables except for one.”

He also revealed a surprising similarity between plant science and high fashion – a little brand name recognition goes a long way.  Thus, the pricey Conviron E15 growth chambers (which cost about $30,000) or Percival incubators are worth every dollar if they help a researcher establish credibility with a publication.

I felt very fortunate to get a behind-the-scenes look into the blooming world of plant science on my own campus, and felt nostalgia for my undergraduate days in an introductory biology plant class at UC Davis.  I remember a TA telling me that once you start learning plants, it gives you whole new way of looking at and appreciating your environment, even if it’s the landscaping around campus.  Now I can say I also have a whole new appreciation for the rooftops on Science Hill!

Thanks, Jim, for a great, informative tour!

Pitcher plants wait to catch a meal at the Thimann Lab greenhouse (photo: E. Loury)

This past weekend I willingly deprived myself of sleep in order to participate in Science Hack Day in San Francisco.

What is a Hack Day?

Well, a hack is a quick solution to a problem. Not necessarily pretty, but probably clever.

A Hack Day is usually a 48 hour event where people with ideas get together and make something cool! Wikipedia lists a bunch of hack days around the world. It seems to be a fairly new phenomenon. Science Hack Day was first held in London last year. Since then people have gotten excited and made things with science! (exclamation points are very much part of the culture) in Mexico City, Cincinnati and last weekend in San Francisco for the second time. Upcoming events include Nairobi and Cape Town.

The idea behind science hack day is that there is so much data out there, and so many things to be found, that people can do science or use science in innovative ways through hacking.

Last year’s winningest hack was the particle wind chime. Matt Bellis, a physicist and post-doc at Stanford, led the team. He writes:

The idea was to allow users to take properties of the particles that we observe in our detector (energy, distance from the interaction region, type of detector it is interacting with, etc.) and map that onto sonic characteristics (volume, timbre (instrument), pitch, duration, etc.). In this way, the user can explore the data themselves and find mappings which either make sense to him or her, or are simply more aesthetically pleasing.

I admit that I was not expecting to be of much use at a hack day. I have no experience in software development or coding and very little ability to use tools and build stuff. But the website said “If you’re a coder, designer, scientist, hacker or just an enthusiastic person with good ideas, Science Hack Day is for you.” I wasn’t sure that I had good ideas, but I could do enthusiasm.

Emails from Ariel Waldmen, the founder of Science Hack Day SF, repeatedly emphasized that I didn’t even need to have an idea before coming. And that eavesdropping on other people was completely acceptable. So I went.

I wandered around the morning of the first day, introduced myself to people and tried to think about how I could be useful. Everyone was very friendly, very enthusiastic and full of ideas.

After inspirational talks I found a couple of young women who won me over with their NCBI ROFL shirts. We were going to create a walk-in, interactive model of a cell, but didn’t think of a satisfactory way to accomplish that over lunch. Instead we turned to the group behind us and decided to help with their idea: create a synesthesia machine to override our everyday senses.

Synesthesia is a mixing of the senses. Synesthetes might report seeing green when they read the number 4, feeling a strong impression of a particular shape when they eat ice cream  or tasting raspberries every time they listen to the third movement of Beethoven’s Moonlight Sonata. Scientists used to believe that this was just a strong memory or that people were making up the sensations. But recent studies show a neurological basis. This study found additional activity in the brain of synesthetes corresponding to their sensations.

The project was based on an idea by this guy:

I asked our fearless leader to tell me about his idea to create a synesthesia machine. He responded via email:

There’s a strong evolutionary pressure to optimize our perception of the world to emphasize information that makes a difference to our survival. This means that we necessarily under-appreciate a large amount of the information in the world, that is, we ignore much of reality. The goal was to short-circuit the pre-processing systems in our visual cortex by sending visual input into an inappropriate sense, the sense of touch. The hope is that the resultant synesthesia would allow us to appreciate a different slice of reality to the quotidian.

Hacking this idea did take us most of the time. I stayed up until 3:30 a.m. and I loved it.

Lil modeling the placement of speakers.

We used a webcam to capture an image and translate that to a 12 pixel square. Each pixel in the square would register the image as either white or black. That would translate to an “on” or “off” code transmitted to an Arduino –”an open-source electronics prototyping platform based on flexible, easy-to-use hardware and software.” The Arduino was wired to small, cheap speakers sewn on the inside of a full head mask. So the visual input was translated to vibration (and sound) on your face!

Initially, we thought we could design a vest lined with the speakers. I was ready to try and modify a thrift-store purchase into a tight fitting garment. That probably would have been beyond my sewing ability. We decided that a mask would be a more visually striking design.

Lil found a pattern online of a bondage mask. Yes, I know … but we needed something that would keep the speakers in contact with your face. I didn’t find a good pattern for spiderman masks, so bondage mask pattern it was.

Other members of the team worked on coding. I have very little idea what goes into software programming, so I don’t know what they did, but they did it well.

We also needed to wire the Arduino to the speakers, something that required soldering and some electronic-building knowledge. I remember building a tiny robot using a kit when I was younger, so I did get to try my hand at soldering. Though I am not an expert, my skills in that area improved under the tutelage of another member of our group (Parker, who was also my old friend from college).

I think was was most remarkable was the way each of us in the group was instrumental in getting to the finished product.

The final product was…amazingly creepy. We call it Syneseizure. It may possibly be the next superhero or supervillain.

Check out our project’s blog for more photos, a link to the code we used, video of the first public test and video of our presentation at the end of the hack day. Our hack won the People’s Choice award!

The other hacks were incredible. From a globe with a laser inside that tracked the movement of the International Space Station, to a drinkable DNA extraction (with Bacardi 151 and strawberries!), there was some seriously cool things going on.

I had a great time. Thanks so much to the organizers who worked to keep us hacking and fed! They did so much. Here is a time lapse video of the 8 hours of set up at the space. And some more photos of the day.

More reading:

An article from Scientific American about synesthesia.

A website about synesthesia for kids, from the University of Washington.

The American Synesthesia Association

One minute I’m milling around the dock of the Santa Cruz harbor, the next minute I’m hurtling out to sea on a 23-foot motorboat named “Aquaholic,” a chilly Pacific gale plastering hair across my face as I shout out questions about crab fishing and scribbling down the answers in a notepad that threatens to be tossed into the drink any second, shortly followed by myself. The driver cuts the engine and all of a sudden we’re bobbing on a glorified cork six miles out to sea. Using all my willpower to keep from tossing my cookies, I watch as a father and his son lower a wiry one-way deathtrap, laden with half a raw chicken, over a hundred feet down to the murky depths below.

A baited crab pot (Photo by Tanya Lewis)

Let’s back up: for our news writing class we’ve been assigned to write an advance on the Dungeness crab fishing season. We’ve been told to interview a crab fisherman, so I call up my classmate Helen and we head down to the harbor to find one. The commercial crab season doesn’t start until Tuesday, so the only guys actually fishing are the recreational fisherman, or “Sporties.” We get to the harbor around 3pm on a Saturday. We figure we’ll find a couple of fisherman, they’ll give us some great quotes about the joys of hauling crab, and we’ll call it a day. Easy as seafood pie!

A crab boat loaded and ready to go (Photo by Meghan Rosen)

Well, the only guy we can find is a man loading up his motorboat with his two sons. Sheepishly, we ask if he’s a crab fisherman, and he replies, “Yes I am. Wanna come out?” The answer’s out of our mouths before we have time to process whether this is a good idea. “Sure!” The rest is history. All-in-all it was…rather educational.

In case you’re not up-to-snuff on your crab knowledge, here’s a little background on the Dungeness crab:

Its Latin name is Cancer magister (literally, “Master of Cancer”). The name “Dungeness” comes from the port of Dungeness, Washington. The crabs are generally light reddish-brown on the back and white to light orange underneath, with a tinge of purple on the legs. Their pincers (chelipeds) are white-tipped and not just for show. (The fisherman we talked to said he uses tongs to handle the cranky critters.) See the photo below right.

Dungeness crab. (Photo from National Archives and Records Administration)

It’s the most abundant crab in California, which is probably why it’s so popular to fish (then again, rats are also pretty abundant and we don’t eat them). The Dungeness lives in eelgrass beds and on the ocean bottom, as far north as Alaska and as far south as Baja California (but aren’t often seen south of Santa Barbara). The males grow to be about 9 inches across, whereas the females rarely get larger than about 6.25 inches.

As a crab grows, its hard shell must be cast off in a process known as “molting.” The shell slits open at the junction of the carapace (front segment) and abdomen (i.e. tail flap) and the crab literally backs out of it, like wriggling out of a sweater. Underneath, a new shell has started growing, but is uncalcified and still soft. The “soft” crab grows rapidly until the new shell hardens. During molting, the crab can actually re-grow missing legs, though it takes a few molts for them to reach normal size again. They molt about once a year.

That’s about all I have to say about these crabs. But there is another kind of crab I want to talk about: the Crab Pulsar!

Recently, a bunch of astrophysicists detected some uber-high energy gamma rays from the Crab pulsar, and the theoretical models have no explanation for it.

A pulsar, by the way, is a highly magnetized rotating neutron star that beams out electromagnetic radiation. A neutron star is formed by the gravitational collapse of a very massive star during a supernova. So basically you have a magnetic ball of neutrons twice the size of the sun spinning around and whipping out pulses of radiation. Pretty insane in itself, if you ask me, but this is old hat to astrophysicists. What isn’t is the high energy of the radiation: gamma-ray pulses with energies greater than 100 billion-electron-volts.

The pulses were detected by the VERITAS (nice acronym, eh?) telescope array at the Whipple Observatory in Arizona. An international group of scientists published a paper about it in the October 7 issue of Science. Nepomuk Otte, a postdoc at UC Santa Cruz, was a corresponding author, and it was his cockamamie idea to look for pulsar emissions in this energy range. Otte’s response?

“To me it’s a real triumph of the experimental approach, not going along with the flow and making assumptions, but just observing to see what there is. And lo and behold, we see something different than what everybody expected.” (as quoted in a UC Santa Cruz press release)

The Crab pulsar was formed by a magnificent supernova in the year 1054, which left behind the Crab Nebula with the pulsar in its center.

The Crab Nebula. (Photo from NASA)

It’s one of the most-studied objects in the sky, spinning about 30 times per second and casting a beam of radiation from its magnetic field. The beam moves around like the beacon of a lighthouse, and Earth detects is as rapid pulses of radiation.

Scientists agree on the broad cause of pulsar emissions: electromagnetic forces created by the collapsed star’s rotating magnetic field accelerate charges particles to close to the speed of light, which emit a wide spectrum of radiation. But the devil’s in the details, which are still pretty mysterious.

After studying the Crab for years, scientists predicted that emissions above 10 Giga eV would die off exponentially. So they were flabbergasted when they found emissions above 100 Giga eV. (The prefix Giga = 10^9, or 1 billion)

~Warning! The next paragraph will make you 20 IQ points smarter. Read on at your own risk~

The conventional wisdom of how the emission works is curvature radiation: a dense electron-positron plasma is created near the polar cap of the pulsar, and the charged particles move relativistically with Lorentz factors   10²10³ along dipolar magnetic field lines, emitting radiation at frequencies that depend on the radius of curvature of the field lines. Phew!

But the results from VERITAS showed something else was going on. It turns out curvature radiation can only explain lower-energy emissions, not the high-energy stuff they observed.

“We really don’t know what causes the very high-energy emission,” said Otte.

(It takes a good scientist to admit they can’t explain something. But it takes a great scientist to come up with a new explanation.)

The scientists think one explanation could be (are you ready for it?): inverse Compton scattering. I won’t go into depth (or I’d be in over my head, to belabor the metaphor), but it involves energy transfer from charged particles to photons. Otte said they still don’t know the details though. They also don’t know if one mechanism explains the radiation at all energy levels, or whether different mechanisms operate at different higher and lower energies.

The next step is to characterize the gamma-ray emission in much greater detail.

So now you know all about crabs and astrophysics. What more is there to life?