Thursday, March 31, 2011

Surf city tsunami

Tsunami surges reach Santa Cruz, March 11 (Image: Flickr/Dan Dawson, used with permission)
The effects of Japan's Honshu earthquake reached as far as Santa Cruz on the Californian coast. On spring break from UCSC's SciComs program, I walked down to the water to gauge what residents have learned.

One week after a tsunami washed into Santa Cruz harbor and ricocheted around the docks, harbor life  has yet to settle. Joggers pass stretches of yellow caution tape. Men in hardhats and plaid shirts clear debris with shovels and high-pressure water hoses. Cafe patrons at the Kind Grind swap yet-to-stale tsunami stories. And, on the docks, Lisa Price's fourth grade class walk among the boats.

Her class – each child snapped into a life vest – is on their annual O'Neill Sea Odyssey outing, run by the company famous for wetsuits and surfing gear. “Every year we love this field trip,” says Price, who teaches at Calabasas Elementary School in Watsonville, Calif. The students learn basics of marine ecology and navigation, such as how to use a compass. Last year her class left the harbor on the Team O'Neill catamaran and saw dolphins and sharks in the bay. This year, as the debris is cleared from both the water and the parking lot, they'll board the dual-hulled boat, but remain dockside.

On the morning of March 11 central California was hit by a tsunami, triggered by Japan's Honshu earthquake. Only six students attended Ms. Price's class that day. The rest stayed home with worried family members. In the Santa Cruz harbor, surges of 5 to 6 feet left $22 million worth of damaged boats, docks and equipment. Now, in the tsunami's wake, the harbor and surrounding community is asking how to return to their routine, and which lessons should be drawn. Nine boats sank during the tsunami and two are still missing, presumed sunken. Dozens of others need repairs or dismantling.

At the boat works, Tom McKervey fields phone calls from anxious  owners. “Yeah, you're on the list – twice for some reason,” McKervey says. “We'll get to you. We've  got a little triage here – we have to take care of the leakers and the sinkers first.” He replaces the handset, “One of my esteemed customers.”

McKervey, blue eyed and white mustached, manages Aquarius Boat Works – a sort of maritime apothecary and repair store. Above the dusty wooden floors the walls are lined with hooks, ropes and maps. On shelving bins of weights and floats sit next to cans of paint and tubes of Spackling paste. The evening of March 10, McKervey watched news clips of the destruction in Japan. He arrived early at the harbor the following morning to tie down loose boats and riggings. He spent the day on the docks, alternately pushing debris away from boats with a pole and running to higher ground during surges.

“All day long the images of their plight [in Japan] made me think – this is a picnic compared to what  those folks had to live through,” he says. “Here only things were broken. Nobody got terribly hurt.” On McKervey's right hand, his thick middle finger holds a row of stitches. “I got a little cut out of the deal,” he says, dismissing it. He believes he will see a change in the local mix of boaters as a result of the tsunami damage, that is his real concern.

Santa Cruz hosts power boaters, sport and commercial fishermen and sailboat lovers. “Some of these folks are working towards the dream of sailing off into the sunset,” he says. And, while it's prominence has diminished, Santa Cruz is still a racing port. “I'm sure the harbor is going to shrink, both in people and boats. Many folks could only marginally afford boating before.” McKervey hopes the harbor will design a faster alert for boat owners, perhaps with a telephone chain, instead of relying on TV and radio. If more people had known sooner, he says, they could have waited out the swells in the open ocean.

Residents nearby responded to the tsunami in ways typical of Santa Cruz. On the day, surfers paddled out, hoping for waves worthy of a Japanese woodblock print. Onlookers crowded the bridges stretching over the harbor, boxes of pizza and six packs of beer at their side, shouting encouragement to McKervey and his fellow workers. The next week, a crowd of more than 100 packed the Community Room of the Santa Cruz Police Department to discuss preparations for the next tsunami.

Some wanted to know, street-for-street, how safe their houses were. Some wanted to know where to watch the waves roll in. Steven Ward of the University of California, Santa Cruz said he understood tsunami curiosity – the desire to head for water – and suffered from it himself. But, addressing the crowd as a geophysicist who studies tsunami's, he urged caution. “Scientists understand the general concepts, but its hard to predict how severe surges will be – especially in real time,” Ward says. “You might expect more of scientists than we can give.”

This is both humbling and frustrating. “My feeling,” says McKervey, “is that these events show us we're pretty insignificant – it reminds me to be grateful I'm alive.”

Watch a video of the tsunami, posted on YouTube by the Santa Cruz Sentinel:

Thursday, March 24, 2011

Music to write to: Andrew Bird, The Decemberists & Afriki Djigui Theatri

Montreaux Jazz Fest
Montreaux Jazz Fest/D. Venton
Santa Cruz is a wet, windy, stormy place this week. This prevents me and my fellow SciComrades from venturing outside while we're on Spring Break. Surely this isn't legal. So, as the rhythm of the rain pounds on my roof persistently, I’d like to offer rhythms of a different nature: A listing of my favorite music and artists to listen to while writing. Please submit your own favorites in the comments.

The best artist I’ve found to write along to is hands down, violin bows up, Andrew Bird. His music is beautiful, looping and lyrical. Something about his dual continuity and innovation help me gather momentum -- particularly if I’m having trouble getting started.

See him solo and live and you can watch as he builds multi-track songs, one element at a time. He records violin-plucking for the beat, whistle-melodies for motifs, and begins to sing. All the while your eyebrows gradually migrate to the outside edges of your forehead. The man has talent.

Catch a live show, if you possibly can, or watch a great example here (if you only watch one of the videos in this post, pick this):

When I’m working for several hours, I often have Andrew Bird on a continual loop in my iTunes. Below, the YouTube Andrew Bird playlist. Particularly addictive tracks include “Thank God it’s Fatal,” “Operation,” “Sythian Empire” and “Mitosis.”

I am also a Decemberists fan, devoted and devout. During the month of February I listened to their new album, The King is Dead a lot. The band (featured in a recent Talk of the Town, “No. 1”) has an ability to make every genre they turn their instruments irresistible. They also have a fantastic vocabulary, employing words such as “palanquin,” “odalisque,” and “roustabout.”

If you are a Decemberists neo-phyte, and unafraid of the idea of good country music, give the opening track of their latest album a try:

And if you’re willing to go for the serious honey-tonk:

Otherwise, an easier entry point might be The Crane Wife (loosely based on a Japanese fairy tale) or The Hazards of Love (a total rock opera, a la Deep Purple). These folks are also *just fantastic* live.

There is also something great about listening to music sung in a language I can’t (or can just barely) understand. My favorite breed of this is music from French-speaking Africa. I’ve poked around the International section of iTunes’ radio offerings and have settled on Afriki Djigui Theatri (also available here). I even like the commercials. I understand just enough of the French to stay amused, without growing annoyed at the advertising.

But I don’t want this post to be one glowing review after another. So let me say that, contrary to their name, Muse is lousy to write to. And while they put on a great light show (see below) I also think they’re pretty lousy live.

Muse in Lyon, France/D. Venton
Just to insert one more complaint, this non-stop rain makes me wish all the more that I was in Austin, Texas listening to music at South by Southwest. This wish might be an impossibility -- among other obstacles, the festival ended four days ago -- but that makes the longing only more acute. A great listing of SXSW music to pay attention is here on NPR's music pages.

Now that I’ve compiled my list, and have offered you more links than you can comfortably process, I wonder what White, Zinsser, and Blundell would say about my habit of scribbling with tunes in the background. I’ll look into it and get back to you. Meanwhile, send me what you write to either below or at danielle.venton[at]

Tuesday, March 22, 2011

Primordial Soup’s Missing Ingredient May Be Sulfur

(I had two stories up on yesterday, here is the second one for you!) 

A fresh look at forgotten vials from Stanley Miller’s primordial-soup-in-a-bottle experiments implies that volcanoes seeping hydrogen sulfide helped form some of life’s earliest ingredients.

Sulfur’s presence makes it possible to synthesize a greater variety of amino acids — the molecules that link to form protein chains — and gives nascent life a larger palette of chemicals from which to select.

“When you are analyzing old samples, you always hope in the back of your mind that you are going to find something really cool,” says primary author Eric Parker, a graduate student now at Georgia Tech.
“It was a pleasant surprise to see such a large array of different amino acids and amines.”

In Miller’s classic experiments, dating from the early 1950s, electricity — standing in for lightning — zaps a few basic chemicals, water, methane, hydrogen and ammonia, to simulate the atmospheric conditions on Earth before life began. Miller became famous for showing that simple chemicals could be combined with relative ease to form some of the building blocks of life.

This 1958 experiment, originally unpublished and revisited March 21 in the Proceedings of the National Academy of Sciences, marked Miller’s first inclusion of hydrogen sulfide, the chemical that makes rotten eggs smell and a prime component of volcanic gas emissions, in the primordial mix.

Using modern chemical analysis techniques, Parker’s team found 23 amino acids, seven other compounds and four amines, a breakdown product of amino acids. This was far more than typical analysis of past samples, which yielded five to 10 amino acids. Several of the amino acids were synthesized for the first time, including methionine, a required building block for many proteins in animals, plants and fungi.

The newly identified collection of amino acids is also similar to those found in meteorites, meaning sulfur may have help assemble life’s ingredients off this planet, as well as on.

Sandra Pizzarello, an Arizona State University chemist who was not involved with the study, agreed with Parker’s chemical detective work. She noted, however, that all experiments seeking to synthesize prebiotic chemicals are limited.

Earth’s early atmospheric conditions aren’t known, and the reactions in this experiment could only have happened near a source of sulfur. On a primordial Earth, that would have meant volcanoes. Whereas Miller originally focused on chemical reactions in the atmosphere, the primordial soup may have gathered in a volcanic bowl.

Volcanic origins were suggested by a 2008 reanalysis of another forgotten Miller experiment conducted by Jim Cleaves, a geochemist at the Carnegie Institution of Washington, and Scripps Institute of Oceanography biochemist Jeffrey Bada. Both are former students of Miller, and plan to revisit more of his old experiments.

“Miller was a real packrat. He didn’t throw anything out,” said Cleaves, Miller’s final lab student and inheritor of the lab. “Sitting on the shelf was this box, I thought, ‘I don’t know what these are, but I can’t bear to throw them out!’”

Images: 1) Stanley Miller in his UC San Diego lab in 1970/UCSD Archives.

See Also:
Citation: “Primordial Synthesis of Amines and Amino Acids in a 1958 Miller H2S-rich Spark Discharge Experiment.” By Eric T. Parker, H. James Cleaves, Jason P. Dworkin, Daniel P. Glavin, Michael P. Callahan, Andrew D. Aubrey, Antonio Lazcano, and Jeffrey L. Bada. Proceedings of the National Academy of Sciences U.S.A., Mar. 21, 2011.

Monday, March 21, 2011

Robot Swarms Could Help Search for Life in Martian Caves

Robot Swarms Could Help Search for Life in Martian Caves

(Latest story from Wired Science.) 

Autonomous swarming robots, programmed to search like honeybees, could be the best strategy to explore caves on Mars that may harbor life.

Methane traces in the Martian atmosphere point to undiscovered activity – whether geological or biological – lurking beneath the surface. “Something interesting is going on down there,” said Áron Kisdi, an engineer at the University of Southampton, UK. “We just need to find it.”

In a paper Mar. 3 in Acta Astronautica Kisdi presents a strategy that he believes offers the best way for robots to search large expanses of Mars for new caves, maximizing search area and minimizing search time.

In 2007 NASA’s Mars Odyssey spacecraft found seven large holes in the surface – too large and deep to be explored with rovers. Odyssey’s resolution isn’t fine enough, however, to reveal smaller caves.  And these, if found, could be more accessible to rovers, with shallow entrances and narrower shafts.

“We have sent robots to mars a few times now,” Kisdi said. “But we’ve only seen a small fraction of
 the planet.”

For his swarm search strategy, Kisdi envisions using a rolling, jumping robot, Jollbot. A Mars lander would release 40 to 60 swarmbots to autonomously and randomly scout for caves, in the same way bees hunt for nesting sites.

When a robot finds a cave – sensed by a difference in temperature – it returns by the shortest route, the bee line, back to the lander. It wirelessly uploads the cave’s coordinates and temperature readings to the lander. Then it checks the information uploaded into the lander by the rest of the hive and decides to either start a new search or visit a cave discovered by another robot. If it also approves of a spot, it informs the lander and the process begins again.

Within a few iterations, the group comes to a consensus: either enough bots deem it a good site to point out to mission control, or interest peters out.

The simplicity of this strategy, Kisdi said, allows for the swarming robots to use the bulk of their power on locomotion, rather than programming, and to be cheaper to build. It also ensures that a larger, more sophisticated rover sent in after the bots won’t waste its time on uninteresting places.

“And if you lose a robot,” he said, “the search isn’t over.”

In a report released Mar. 7, a panel convened by the National Research Council asked NASA to give the Mars Astrobiology Explorer-Cacher the highest priority of its large missions. This project, the first of three, would collect samples from the Martian surface for analysis. But the report stresses the mission should only proceed if costs can be cut to $2.5 billion – $1 billion less than current independent estimates. This could give Kisdi’s search algorithm a better chance of, one day, seeing the methane of Mars.

“The hard thing about exploring Mars is providing power to robots on the surface,” said David Beaty, Mars Program Science Manager at NASA’s Jet Propulsion Laboratory. “The surface area of Mars is equal to the surface area of Earth’s continents. Traveling between one cave and another might be a distance of hundreds of miles.”

Beaty isn’t aware of any swarming robot search models under current development at NASA. But, he says, if the robots in Kisdi’s search model were long-lasting and mobile enough, the idea has potential. In Kisdi’s current simulation 50 swarm robots cover an area of 300 square meters in about five days. The area can be expanded by adding more robots with a longer search distance.

“I’d like to start developing the hardware next,” Kisdi said. “I plan to keep working on the idea until the next call for proposals on Mars missions.”

Image: A candidate landing site for Mars Science Laboratory, Curiosity, captured by the HiRISE telescope. Credit: NASA/JPL/University of Arizona.

See Also:
Citation: “Future robotic exploration using honeybee search strategy: Example search for caves on Mars.” By Áron Kisdi and Adrian R.L. Tatnall. Acta Astronautica, Mar. 3, 2011.

Thursday, March 3, 2011

4 New Species of Zombifying Fungus Found

(Because I take my charge to bring you the latest in funky insect news very seriously, my newest piece from 

Four new species of brain-manipulating fungi that turn ants into "zombies" have been discovered in the Brazilian rain forest.
These fungi control ant behavior with mind-altering chemicals, then kill them. They're part of a large family of fungi that create chemicals that mess with animal nervous systems.

Usually scientists study these fungi as specimens preserved in a lab, said entomologist David Hughes of Pennsylvania State University, co-author of a study March 3 PLoS ONE. "By going into the forest to watch them, we found new micro-structures and behaviors."

Once infected by spores, the worker ants, normally dedicated to serving the colony, leave the nest, find a small shrub and start climbing. The fungi directs all ants to the same kind of leaf: about 25 centimeters above the ground and at a precise angle to the sun (though the favored angle varies between fungi). How the fungi do this is a mystery.

"It's related to the fungus that LSD comes from," Hughes said. "Obviously they are producing lots of interesting chemicals."

Before dying, ants anchor themselves to the leaf, clamping their jaws on the edge or a vein on the underside. The fungi then takes over, turning the ant's body into a spore-producing factory. It lives off the ant carcass, using it as a platform to launch spores, for up to a year.

"This is completely different from what we see in temperate zones where, if an insect dies from a fungal infection, the game's over in a few days," Hughes said.

"The fungi rots the body of the insect and releases massive amounts of spores over two or three days. But in the tropics, where humidity and temperature are more stable, the fungi has this strategy for long-term release."

Of the four new species, two grow long, arrow-like spores which eject like missiles from the fungus, seeking to land on a passing ant. The other fungi propel shorter spores, which change shape in mid-air to become like boomerangs and land nearby. If these fail to land on an ant, the spores sprout stalks that can snag ants walking over them. Upon infecting the new ant, the cycle starts again.

Chemicals from this global group of fungi, known as Cordyceps, have been a part of traditional medicine for thousands years, and part of Western medicine for the last 50.

Organ transplant patients, for example, receive ciclosporin — a drug that suppresses the immune system, reducing the chance the body will reject the new tissue. Chemicals from this same fungal group are also used for antibiotic, antimalarial and anticancer drugs.

The fungi help the forest by keeping ant populations in check. "All of the problems with global ant infestations, for example the Argentine fire ant," Hughes said, "is because the ants have escaped their natural enemies. Then they become a pest."

These fungi need a precise level of humidity to survive. As global temperature changes, the forests where they live are drying. Hughes and his colleagues are now studying the decline these fungi.

"We're worried we'll see the extinction of a species we've only just managed to describe."

On the following pages are more photographs of zombifying fungi in action.
<< Previous | Next >>

All images: David Hughes, Pennsylvania State University

See Also:

Citation: “Hidden diversity behind the Zombie-Ant fungus Ophiocordyceps unilateralis: Four new species described from Carpenter ants in Minas Gerais, Brazil.” By Harry C. Evans, Simon L. Elliot, David P. Hughes. PloS One, Vol. 6 No. 3, March 2011.