Deathbed conversations: tell me about the plants

Photo of Solorsano, by J. P. Harrington.

Dramatic deathbed scenes are all too rare in news stories. So I'm happy that my story in today's Santa Cruz Sentinel and the San Jose Mercury News has one.

Ascencion Solorsano de Cervantes was the last member of the Amah Mutsun tribe versed in the traditional ways of medicine. People from hundreds of miles away sought her care.

In the summer of 1929 at age 83, Solorsano, the last fluent speaker of the tribal language, and a longtime resident of Gilroy, felt death approaching. To prepare, she moved to her daughter's Monterey home, bought a new black silk dress for burial and called her family close to say goodbye. But life had more in store. John Peabody Harrington, a Smithsonian linguist who spent his life recording native languages and customs, heard of Solorsano's illness and rushed to her.

Read the rest.

In the UCSC Arboretum

Greetings from the depths of December

Hello sundry folk! To put an end to the near-criminal level of neglect I've shown this blog, let me give an update. The most important news is that I survived the fall quarter of the SciComs program (along with my nine SciComrades). There was some gnashing of teeth and wailing. But overall I think my molars are in good shape. I haven't made an appointment to see a dentist yet at least. 

We start again January 4, and will work on features and profile writing. But we've not been idle during the break. As proof let me share what I've been writing during the last few weeks.

Most of us were at the American Geophysical Union meeting in San Francisco last week. This was an astronomically-sized meeting of ground-shaking, world-exploring, climate-modeling, fossil-uncovering research. We were paid bloggers and, while fun, this was a little rough. We needed to turn the posts around quickly and we were covering subjects that were far removed from our academic fields. We had little time to speak to the researchers (if we had any). But what doesn't kill you will either give you indigestion or make you stronger. 

A little collection of my posts for you, starting with the most recent first: 

New cockpit for Alvin, the famous deep sea diver!

Between sessions last Friday, I hope you visited the exhibition hall one last time. Past the jewelery stands selling fossils and geodes and booths selling maps and drilling equipment, you may have spotted a minor celebrity–a little machine famous for great science.

Spurred by climate change, plant die-offs could wreak havoc on Tibetian lifestyle
For thousands of years the traditional herders of Tibet have lived among mountains, lakes and grasslands. Their livelihood– raising yak, sheep, and goats on the largest and highest plateau on the planet–is a precarious one.

Selling the science of geoengineering
It is a shocking idea, a terrifying idea, yet a mesmerizing idea–and it could just save the planet.

3D movies of the Earth as it changes

No sooner did I wish for a 3D movie at AGU, than I got one. 

What do you want to see on Mars? Tell HiRISE!
The most powerful camera ever sent to another planet wants to know what you’d like to see.
 

New eyes on the ocean
A global flotilla of diving robots have their eyes trained on the seas. 

X-ray vision: Space weather and the Solar Dynamics Observatory

In February, NASA launched the Solar Dynamics Observatory (SDO), an Earth-orbiting spacecraft, dedicated to investigating the Sun and it’s effect on Earth and space weather.

I also wrote a story for the newspaper based on a NASA press release at AGU. 

Space agency helps growers: NASA satellite project can check individual plots of land

Growers in the Salinas and San Joaquin valleys are about to get help from above.

More excitng news-paper related updates coming tomorrow!

Training to be a cage-fighter, er, writer

(A re-post from our class blog A Tale of Ten Slugs.)

Among the lush pickings of memorable lines from the 2004 movie Napoleon Dynamite, one of the best is Kip’s to his brother:

“Napoleon, don’t be jealous that I’ve been chatting online with babes all day. Besides, we both know that I’m training to be a cage-fighter.” (Video from Hulu, if you’re rusty on the scene, feel free to skip.)

Well go Kip, I say. This line bubbled to the surface of my mind today when I was watching an interview with Truman Capote, dating from the mid-60s.

By all means skip the video above, but this one (non-embeddable, unfortunately) which I found via a Twitter lead is worth the time. (Yes, Capote’s voice is obnoxious, but deal with it and it’ll be worth it.)



Capote discusses becoming a writer, his book In Cold Blood and how his writing style change over time. His opening sentence is especially wonderful to keep in mind:

“If you are going to have a genuine career in the arts, it’s exactly like being a prize-fighter or a concert pianist. It isn’t something that you just take up one moment and drop the next. It’s an act of continuous concentration on your work and building the thing more and more toward its larger possibilities.”

It’s easy to forget that even the most excellent writers had to develop their skills. I’ve been slowly working my way through listening to In Cold Blood on long car rides. Capote is capable of giving the reader a great deal of information through the choicest details. The book’s opening paragraph:

The village of Holcomb stands on the high wheat plains of western Kansas, a lonesome area that other Kansans call “out there.” Some seventy miles east of the Colorado border, the countryside, with its hard blue skies and desert-clear air, has an atmosphere that is rather more Far West than Middle West. The local accent is barbed with a prairie twang, a ranch-hand nasalness, and the men, many of them, wear narrow frontier trousers, Stetsons, and high-heeled boots with pointed toes. The land is flat, and the views are awesomely extensive; horses, herds of cattle, a white cluster of grain elevators rising as gracefully as Greek temples are visible long before a traveller reaches them.

For someone, like me, who reads this and thinks, “How did he do that? How can I do that?” His suggestion of training yourself like a prize-fighter is both a comfort and a rally.

My piece from today's Monterey Herald: The science behind turkey magic

Courtesy of the  State Library and Archives of Florida via Flickr

The science behind turkey magic
Cooking the Thanksgiving bird a mix of physical, chemical reactions
By DANIELLE VENTON
Herald Staff Writer
Posted: 11/25/2010 01:30:43 AM PST
Updated: 11/25/2010 01:30:44 AM PST

In kitchens across the nation today, as cooks prepare the Thanksgiving bird, the oven will be the object of a near-magical transformation.
A raw, unappealing, plucked gobbler will go in. If all goes well, a tender, browned, aromatic wonder will come out.

The change is the result of a host of physical and chemical reactions. For the curious, an investigation into the science of cooking the grand old bird offers useful insights.

Ever had turkey tartare? Not likely. Meat such as beef and fish is tender and flavorful when rare. When prepared properly, these can be relatively clean as well. But undercooked poultry is a tough, bland, bacterial growing ground.

Cooking addresses each problem. High heat kills bacteria. Cooking unravels protein fibers making the meat more tender and easier to chew. Cooking — in particular, browning — creates wonderful scents and flavors that make our mouth water.

Banishing the bugs
Poultry preparation requires special vigilance. An uncooked turkey carries potentially dangerous bacteria on the outside and the inside of the carcass. When turkeys are slaughtered and eviscerated, their intestines are unavoidably punctured.

"When they are cleaned, some of their feces are spread around the inside of the bird, and the outside," said food safety expert Benjamin Chapman, from North Carolina State University.

"The inside of the bird is actually the most contaminated part."

Cooking your bird to an internal temperature of 165 degrees Fahrenheit will kill any bacteria. But, Chapman cautions, turkeys need to be cooled properly. He suggests separating uneaten portions in medium-size plastic bags and laying them in the refrigerator to cool. Leaving cooked meat around for longer than two hours will only invite other bacteria to grow.

"It's quite complicated to prepare a large meal for 10 to 15 people and to get the timing right for everything," he said. "Good safety is important to pay attention to, though, because we see a spike in food poisoning outbreaks around the holidays every year."

Tricky timing
While you faithfully cook your bird to 165 degrees, what is happening to it?

Cooking softens meat by unraveling coiled muscle fibers and connective tissue. But overcooking will squeeze out the moisture in the meat and congeal the muscle fibers, leaving it tough and dry.

Brining a turkey — soaking it in salty water — moistens the meat and infuses salt throughout the bird. Salt allows protein fibers to hang onto more water while cooking.

Cooks should be aware the temperature will continue to rise inside the bird a few degrees, even after it is removed from the oven. Heat from the hotter outside of the bird will continue to transfer inward, so it should be taken out 5 to 10 degrees prior to the desired temperature. A 20-minute "standing time" will redistribute the meat's juices and let some muscle fibers that have contracted under the heat to relax. The turkey is then easier to carve.

Infrequent flyers
One of the reasons the Thanksgiving roast is such a challenge is that turkeys have two very different types of meat — each needing slightly different cooking temperatures.

Turkeys spend most of their life on their feet. Their attempts at flying are rare and pathetic. Their leg muscles are stronger and tougher than the rarely-exercised light breast meat. This is because leg meat stores more fat and pigments. The primary pigment is myoglobin, which helps muscles store oxygen and results in a denser meat.

For full effect, the dark meat needs 180 degrees. Breast meat is best when it reaches approximately 165 degrees Fahrenheit. Alton Brown of the Food Network's "Good Eats" suggests a highly specific 161.
Cooks have several suggestions about how to achieve this temperature differential.

Food science expert Harold McGee, author of "Keys to Good Cooking," suggests securing ice packs to the breast meat while thawing so the different sections of the bird begin cooking at different temperatures. Brown recommends making an aluminum shield to deflect some heat from the breast. Some cooks prepare the bird upside down. The simplest method is probably to cut the legs from the body and cook separately.

Mysterious chemistry
The chemistry of what actually makes a browned bird taste so good is still a subject of some mystery. High temperatures cause proteins and sugars to break down and react with each other. By themselves, the molecules don't have any aroma — they are too large to escape into the air. Our sense of taste is primarily based on our nose, so if we can't smell it, we can't taste it.

But when the proteins and sugars combine under high temperature, they create hundreds of new compounds small enough that we can smell and taste them. Researchers have been cataloging the tempting molecules for more than 100 years. More than 500 have been identified in poultry, and there are new ones to be discovered.

To achieve a brown, tasty crust on your bird, McGee recommends starting out at a high temperature. After the browning is out of the way — and the flavors that make our mouth water have been created — turn down the heat to monitor the bird's internal temperature. Doing this in the reverse — slow cooking followed by high temperature searing — makes it easy to overshoot the target temperature.

Assuming you have achieved scientific perfection with your 20-pounder, pour yourself a large glass of wine. Inhale deeply. See how many of the 500 turkey flavors you can smell. Grab that knife and fork. And have at it. Enjoy!

Danielle Venton can be reached at 646-4358 or dventon@montereyherald.com.

Family wisdom: How to write stories that sell

My mother gave me this wonderful old slip of paper hand typed by my grandmother many decades ago. It is a set of guidelines for “Writing Stories that Sell.” The advice proffered is still valid, so I wanted to share. The charming exception is the section detailing how to prepare your manuscript for submission. What is “pica” if I may ask?

My grandmother fancied herself a bit of a writer. She didn’t write full-time or professionally, however she regularly contributed to her community paper, the Sunland Village Journal. Apparently she even had a column called, “The Cook of the Month.” A surprise for a woman who resolutely shunned cooking. I can’t blame her, though, for taking every opportunity to write. Her specialty, my mom says, were features about decorating and travel. Oh yes, and Bridge, the card game of her obsession.

We have a book of her clippings in my family’s possession. I’ve never read these, though apparently I am mentioned in several columns. My mom said she’d let me take the book back to Santa Cruz with me after my visit this weekend. I can’t wait to deleve in to them.

In class today we reviewed the writing guidelines we’ve learned this quarter. I took notes faithfully. Possibly someday I’ll get to pass them on to my own grandaughter. For the record: 

Couple still very sweet, despite 'honeymoon from hell'

A fun piece I wrote for today's Monterey Herald. -DV

Honeymoon becomes the cruise from hell for Salinas couple

Couple booked passage on ill-fated Carnival Splendor

By DANIELLE VENTON
Herald Staff Writer

Posted: 11/18/2010 01:29:54 AM PST

Updated: 11/18/2010 08:59:14 AM PST

John and Tannya Wallace hold a photo taken of them during... (ORVILLE MYERS/Special to The Herald)

• «
• 1
• »

 

 

John and Tannya Wallace knew married life would come with difficulties. They just didn't know how soon. 

"It was about 6 a.m. and the boat began to lurch. Then it just stopped," said John, 28. "A couple of minutes later we smelled smoke."

The Salinas couple had just left for their honeymoon the evening before. The ship encountered difficulties Nov. 8.

Their first cruise, aboard the ill-fated Carnival Splendor, was a trip Tannya, 22, researched extensively. She heard this cruise line, this specific ship, was the most fun. 

Read more

Of potatoes and pitches

(A reposting of my entry on our class blog: ataleoftenslugs.com.)

Robot laser sharks, we hear, are super newsworthy (Image: Robb Gibbs)

Our class stories appeared on mongabay.com this week. I wrote about researchers who study cheetah fertility with ultra-sonography. It’s gotten me interested in other ultra-sound uses, beyond the realms of reproduction, as I hunt around for interesting story ideas. Any surprise that I came up with a food example?

Check out this wild study in the American Journal of Potato Research (not a joke, this is real), “Detection of Internal Defects in Potato Based on Ultrasound Attenuation,” published online November 11. Not being up to speed on the rapidly developing world of tuberology, I can’t possibly say if this is novel or a big deal for spud studies. What it does show, however, is the interconnection between multiple science branches and that, if you can measure it, you can study it.

Journalism is similarly constriction-free. Nearly everything can be written about, with a few caveats. You must be able to justify what you want to write about. This week I’ve run a few story ideas past editors and I’m learning that pitching is an elusive art! No doubt a very valuable lesson (along with patience). An interesting topic and the enthusiasm to pursue it is not enough. You need the maelstrom of news values.

How to give a spud a sonogram

Thus, “Researchers hunt rotten potatoes, image human embryos on the side,” is not necessarily a story.
But, “Potatoes capable of live birth, fed tomorrow to just-discovered robot laser sharks, in your backyard” would be a great story. (*Sigh*)

What I really want is a study titled, “Detection of Internal Defects in Story Pitches Based on Ultrasound Attenuation.”

The wordy and nerdy luminaries of the science-writing world

My brain, personal network and Twitter followers were expanded over the weekend as I attended a science writing conference. An added perk -- I was invited as a guest poster on a Nature Education blog. Read my report from the conference:

Guest Post: Learning from the Luminaries

This weekend, New Haven, Connecticut, glowed with the wordy and nerdy luminaries of the science-writing world. They were drinking coffee like water, exchanging business cards like blackjack dealers, and hobnobbing amidst dinosaur bones.

I was at ScienceWriters2010, a joint meeting of the National Association of Science Writers Annual Workshops and the Council for the Advancement of Science Writing's New Horizons in Science Briefings, hosted at Yale University. While many of the names present were from the heights of the science writing, there were also more modest people like me (i.e., students).

Read more

Bacteria are the stars of the show

Thoughts on Newspapers

My first contribution to the SciComms class blog (at http://scicomucsc.wordpress.com/)
In my first video blog, I talk about H. L. Mencken's thoughts on newspaper work: "a grand, gaudy time."

Seaside nonprofit refurbishes computers for needy

(Written for the Monterey Herald, published 10/07/2010.)

Christian Mendelsohn is ensconced among stacks of computers, motherboards and hard drives.

On the upper shelves nearby, rows of flat screen monitors are stored sideways, like an encyclopedia set of computer screens. The shelves below hold neat plastic bins labeled "ethernet cables," "power cords" and the like.

Mendelsohn is surrounded in his Seaside office by computer equipment. He is eager to distribute it to those who usually couldn't afford it through his nonprofit company Loaves, Fishes & Computers.

"Right now we have about a two-month turnaround time," said Mendelsohn, 32, while he leafed through a binder full of applications for the computer systems. "We have the supply to take care of the demand. But we're lacking manpower, we're lacking space and we're lacking funds."

Mendelsohn started the nonprofit in April 2009. The charity takes unneeded computers from organizations and individuals, refurbishes them and sells or gives them to the needy and computerless. Those who qualify get a computer, monitor, printer, mouse, keyboard and, if needed, set up and training. Depending on their income, recipients can pay $50, $60 or $70 or, if they like, they can spend six hours in volunteer work.

Loaves, Fishes & Computers is funded primarily through Mendelsohn's work repairing computers for clients. The group is an incorporated nonprofit, Mendelsohn said, and expects to receive tax-exempt status from the IRS in four months to nine months.

Refurbishing work is done by volunteers, two of whom come in every day during the work week.

"Like me, they love computers and like to do good," Mendelsohn said.

Mendelsohn would like to see Loaves, Fishes & Computers expand. In the Seaside office, they restore and turn out three to five computers a week. Two years from now, Mendelsohn would like it to be 20 computers a week.

"I have a vision of LFC expanding in to a larger area, where we'd have more repair space, space for volunteers and a computer lab open to the public," he said.

In their current space, there is only room for two people to work.

"Library labs get filled up and time on their computers is limited," said Mendelsohn. "Some students would like to volunteer as refurbishers. This would be a way for them to give back to the community and learn how to fix computers for themselves or for work."

Mendelsohn is starting a recycling and decommissioning service to remove e-waste of local businesses.

"We have a lot of computers in the area going to e-waste," said Topher Mueller, K-8 technology coordinator at the Carmel campus of Stevenson School, who helped donate 12 computers.

"Half of those might be too old to be useful, but the other half should be kept out of e-waste, which is becoming a huge environmental problem. They can be put to good use. There is a gap in opportunities between people who have computers and those who don't. He is bridging that gap," Mueller said.

"It's best to keep these computers in the hands of students and out of e-waste dumps," said George Ball, property coordinator at CSU Monterey Bay, who aided in the donation of 80 computers.

"The work he is doing is phenomenal," said Mueller. "He's filling a niche in the community that to my knowledge no one else is doing."

While Mendelsohn's work might fall short of miraculous, it is nonetheless appreciated by recipients.

On the wall of his crowded office, Mendelsohn looks up at a painting given to him from an artist who received the second computer he refurbished. In the picture, Jesus is feeding the masses with loaves of bread, baskets of fish and, down in the corner, a little collection of laptops.

Danielle Venton can be reached at 646-4358 or dventon@montereyherald.com.

---

Loaves, Fishes & Computers
A nonprofit in Seaside offers refurbished computers to those who normally couldn't afford them.
· A computer setup (including monitor, printer and setup and training) costs from $50 to $70, depending on the consumer's income.
· Consumers can also get computers in exchange for six hours in volunteer work.
· The wait time for a computer is two months.
· To apply for computers or make donations, call 383-0412 or see loavesfishescomputers.org. Printers are especially in demand.

Newsflash!

I'm now at UC Santa Cruz enrolled as a graduate student having the (busy) time of my life. Feeling very inspired to get this blog up and running again, I'll start by sharing a few of the things I've been doing recently.

As a start, the ten class members of SciComs 2010 were served a hefty dose of self reflection, having to write biographical blurbs (see below) and our own obituaries (for the hearty, upon request).

Aside from being useless behind a microscope, I’m in science writing for the variety. Like many a writer before me, I love language, learning and talking about science. I love new experiences that deepen my understanding of the world and its people. Science writing gives both author and reader access to every field touched upon by research, which is to say, every field there is.

I’ve worked in science communication from many places: the redwoods of Northern California, the ponds of Cape Cod's National Seashore and the caverns of the Large Hadron Collider, the largest particle accelerator, at CERN in Geneva. Every new place, every new project, teaches me something and broadens my perspective. The world will always have something new to teach us, science writing allows me to remain its student.

When I'm not envisioning my future demise, I'm writing at the Monterey Herald, a local daily newspaper. Working on a big piece tomorrow, look for it here in a few days.

Migratory amimals

Sandhill Cranes at Sunset
Originally uploaded by gary woody photography

Like a migratory bird, bent on following the sun, I've landed in my new wintering grounds or, in this case, summering grounds. For the last month and a half -- by coincidence for the same amount of time this blog has gone unupdated -- I've been back in Northern California, in a drastically different environment than urban-dwelling, full-time working, CERN life in Geneva.

To my surprise leaving Geneva, when it finally came, was a relief. I had spent the previous three weeks in that intensified mode which always takes over when you are about to jump in to a big geographic change: saying goodbye, organizing the minutiae, desperately savoring the place while you still have the chance.

I quite like the image, I must say, of myself as a migratory animal. Where ever these animals are calling home they contribute to, and get what they need from, their area. Where ever they are they have a purpose, a role in their ecosystem (one beyond collecting fridge magnets from all the capital cities of Europe). For example, now I'm living with extended family in Napa County, California. This unit of my family currently includes young kids. Part of my "ecosystem services" in Napa involve diaper changing and dinner cooking. While it is not what I want my life to look like forever, at the moment, its not so bad. I know in time I'll migrate on.

One of our favorite migratory mammals along the whale-watching Californian coast is the Humpback. These whales travel up to 16,000 miles annually, feeding during the summer in fish-rich sub-Arctic waters, and traveling down to tropical environs to calve and over-winter. Salmon also migrate, spending the start and end of their life in freshwater streams, cruising the rest of the time on the open seas. By coming upstream to spawn, they transfer nutrients from the ocean to the rivers. This helps zooplankton and phytoplankton flourish, which in turn becomes food for the next generation of salmon. The small fry are literally sustained by their parents. Aside from whales and fish, insects, antelope and of course the iconic migratory birds all have second homes. Birds generally eat around a third of their body weight in insects each day -- keeping insect populations in check where ever they are. (Worryingly, many migratory populations have crashed, as the populations disappear they take with them the ecological services they provided. For more read Going, Going, Gone: Is Animal Migration Disappearing?)

When you've lived in many places, you begin to feel less like you are native to anywhere and more like a citizen of the world. You take something from, and leave something in, each place. I'm sure my fellow migratory species would agree with me.

Last day at CERN

I'm in the midst of my last day at CERN. I'm about to leave the office to turn in my badge, keys, get the final signatures and have lunch one last time with my office mates.

Leaving CERN isn't easy, though it is a decision I made and a decision I'm happy with. Sad as I am to leave Geneva, I can't wait to be back in California, back with old friends and back in school.

While I'm clearly not the most dedicated blogger, I'll try to keep this alive, as I can, sharing new tid bits as I come across them. If it is CERN-news that you're after, let me share this amazing little link (CERNlove.org) that someone sent to me the other day. Items discussed? The peculiar signs in the toilets, our decaying buildings, the coffee machines and other hundred other niceties.

It is an amazing place here, someone someday will need to write a cultural history of the place. They would have plenty of material. I was speaking to someone the other day about the different cultures of the Physics and IT Departments. Within those groups, each division -- for example each experiment -- has a unique feel. Dividing things further, each subdetector has its own team and culture. Rivalries (friendly, or at least touted to be) are rife. As long as no one takes themselves overly seriously, it is all a lot of fun. (Physicists?? overly serious?? Never!)

Speaking of which, apparently it is a very serious matter if you do not take care of all of the administrational minutiae of leaving this place, so I'd better head out.

Checklists, complexity and patterns

Shoreline at Santa Cruz, California
Originally uploaded by Oregon State University Archives

If anyone keeping up with this blog hasn't heard already, my life is about to go through a big change. (I'm leaving CERN and Switzerland to go back to California, where I'll study at UC Santa Cruz.)

Standing on the brink of another transition (which I am thrilled about) I've been thinking quite a lot about what I want my future life to look like. And it occurs to me that, while defining what makes a daily routine “good,” a career “good,” a friendship, a book, or even a glass of wine “good” might prove elusive, there are useful things to look for, that will give you a strong indication of its quality. A kind of “checklist of goodness.”

I've been thinking about this because, after reading Atul Gawande's essay “The Checklist”, I'm convinced of their power. I've made many lists for the things I need to do before I leave Switzerland and move back to California. I've made a check list of what I want in my apartment in Santa Cruz that I will (I hope) share with my brother. I have even gone so far as to make a mental checklist of the things to me that indicate a “good day.” Let's turn this checklist from mental to actual, shall we?

Sufficient sleep; sufficient water; time to exercise a little, read a little and think or write a little; fresh good food (including two hot meals, I guess I'm sort of high maintenance); some satisfying work; and some social contact.

People talk about a “perfect day,” a concept which I've also been thinking about and have concluded is downright evil. The strive for perfection is paralyzing. “Perfect is the enemy of good” as Voltaire so astutely noted.

So what makes things inherently good? This is a pretty interesting question. We often have a gut reaction to things. You taste a wine or meet a person and think, “I like it,” “I like them,” “I dislike it,” “I dislike them.” If you never venture beyond reacting to things and people, that's not a terrible problem. But it is useful to examine things a little closer to understand why.

What you like anyway is more appreciated because you can see it more clearly. And appreciation is the mother of enjoyment.

What you dislike, once you understand why, becomes less frustrating. You are better able to navigate the issue as you think and talk about it. You make better decisions as you decide what to do with it or, in some cases, with them.

Want to know where these thoughts stem from? A book I've begun listening to. A book on wine no less. Making Sense of Wine by Matt Kramer. The author makes a powerfully persuasive argument for things that seem to indicate goodness. I quote:

“Inevitably, one comes to the essence of the matter: What constitutes quality in wine? How do you go about distinguishing between what tastes good to you and what is genuinely good? It's not as difficult as it may appear, nor as arbitrary as it sounds. In anything where matters of taste are important there is no one idea, but there can be standards.”

He goes on to say that, for wine, complexity is the single most important standard. He says that humans (and animals too research indicates) find complexity fascinating, possibly because this keeps us surprised and engaged. However, a certain harmony, the existence of patterns, a sort of cohesion, is required otherwise we find the complexity jarring and eventually irritating. Now, I find this idea fascinating. This is why we love studying science, reading Russian novels or seeing patterns repeat in plants and flowers.

Beyond that, he speaks of other needed qualities: balance, proportion, and “finesse” or fine-ness (the quality most elusive of definition, so we'll save that for another time). I put it to you, these are not just needed for good wine, these qualities, this checklist, are what makes anything good. Architecture. Fashion. Literature. A great dinner. Our day and, yes, our life.

Now, speaking of exquisite, balanced, fine, well-proportioned food, the Japanese do quite an amazing job. Mark Bittman (who I am adopting as a food fairy god-uncle) has inspired me with his column in this week's NYTimes. This is to be the afternoon's experiment.

(Photo above found here.)

My travels back from Sweden

Last week I was drinking mead in the land of Vikings for a conference. It was the last and final big event for the project I work for. As noted by Steven Newhouse, our technical director, in the closing session on Thursday, “We are ending with a bang.”

Late on Wednesday, April 15th a volcano in Iceland (known by the festival of letters “Eyjafjallajökull”) had unexpectedly erupted. It spewed plumes of volcanic ash into the atmosphere – at just about the elevation planes fly.

It is rare – and welcome – for a natural disaster to have so little impact on human lives and suffering. What misery there was being mostly limited to interrupted travel plans and inventive, lengthy journeys home. What journeys we had though!

Many of us spent a large part of the weekend following the forum sending flurries of e-mails to each other, trying to access websites that were forever crashing, making phone calls to lines that would not pick up, trying to get news of our workmates, and assuring ourselves that everything would clear up in a day or two. When it didn’t a group of us from the Project Office – who had considered 1) renting a car, 2) hiring a coach, 3) hitchhiking, 4) waiting it out or 5) surrendering to fate and starting a new life Stockholm (well, me anyway) – we finally settled on a plan of some daring.

After an epic queue at the train station on Sunday (no tickets for sale until Tuesday, and then only out of Sweden) one section of the team braved the line for coaches – seeking overnight passage to Copenhagen. Another contingent from their hotel rooms had found a means to book train tickets on an obscure section of a website and began booking the legs Copenhagen to Hamburg to Basel to Lausanne to Geneva. Assuming we could get to Denmark, it would work.

We needed four tickets for that evening. By a kind of miracle we got the very last four. We called Bob (who was poised to get the train tickets, assuming we could get the bus tickets) with the good news. No dice – it seemed. We wouldn’t be able to leave Copenhagen till Tuesday. We’d might was well take a car. We gave the bus tickets back – hoping someone else could use them.

A quarter of an hour later Bob called again – he could get the tickets. I rushed back to the coach counter. The woman I’d handed the tickets back to had thrown them away, since they couldn’t be resold. She was afraid she wouldn’t be able to find them again and began to shake from fear and stress (this was a real low point of the journey for me). Happily, they were still in a dust bin in the back office.

With bus and train tickets (first class, no others were available) we set off from Stockholm at 10:45 p.m. at night. I had hoped that my days of long-distance bus travel had departed along with their heyday: my early 20s. But here we were again . . . in for a eight hour ride (my record, aged 22, is 27 hours from Barcelona to London). As an added pleasantry, the bathroom in our coach was broken. Specifically, the toilet was overflowing. Spewing Eyjafjallajökull-like out of the door and in to the central isle. Sheets of water slid forward whenever the bus downshifted or came to a stop. Heaven help us if we had been in flip-flops.

None of us slept well during the night. Catherine Gater, EGEE dissemination manager, shared a row with a woman who crashed, coma-like, for the first half of the journey (literally climbing over her left her undisturbed). At about 3 a.m. the woman turned particularly (one hates to use the word obnoxiously) chatty.

“You know, I was eight months pregnant before I suspected something was up.” “I can’t wait to get home to my guinea pig and my fiancé.” “How old are you? That’s a nice iPod.” Upon which Catherine said, “Yes, isn’t it?” and stowed the iPod in the bottommost reaches of her purse and tucked the bag away.
Upon arriving in Copenhagen we felt like we’d been spewed from a volcano ourselves, though it would still be a long while before we reached something like land.

We had first class passage on the train to Hamburg, the only available, but had to stand, perch on ledges or sit on the floor anyway – the train was woefully oversold. In Hamburg we had about 5 minutes to change platforms (most of the train seemed to be trying to make the same connection) but got on it somehow.

From there the day turns foggy for me. We changed trains about half a dozen more times. Sometimes making the slim connecting time, sometimes not. At about dinner time, cruising through Southern Germany, we found an empty table in the dining car. More specifically we, er, I coerced a lingering couple to give it up. To celebrate having made it thus far we ordered some champagne, saying how glad we were that we did not have to make the journey alone, with infants, medical conditions or with the continued company of the bizarre woman on the bus.

Following that we made some more train connections, missed some more, got separated in Basel (who knew there were two Basel stations?), had to take a taxi to catch a train from a different station (the driver kindly offered to take us all the way to Geneva for a mere 1,000 CHF. We politely declined. Even if he knocked off 10%? We politely declined again.) In the end, we got home at about 1 a.m. A journey in total of around 26 hours.

Coffee questions

Coffee mania
Originally uploaded by yelalaily

Do you think the folks who first began to cultivate coffee had any idea what they were getting us into?

Coffee is so interwoven with Western and near-Eastern culture that its rightful place is as the flip side of wine: stimulating instead of sedating, steaming instead of cool, bitter rather than sweet, normally taken in the morning rather than the evening. Like wine it is normally found around food, at casual and formal occasions, often is accompanied by a ritual, but seems like a good idea anytime we feel like it. And the second helping is never as divine as the first.

Both encourage dependencies and in excess are clear vices. However, while the benefits of moderation in wine have been proved over and over (not least its anti-aging, anti-oxidative and letting-your-mother-know-what-you-really-think properties) the judgment on coffee is less clear cut.

A dear friend who – when she is not nursing patients – nurses a coffee habit of legendary proportions, once said that she could speak for five minutes and convince anyone that they should never again take another sip of coffee. This, she said, could be followed by another five minutes in which she could convince the same person that they should never let anything come between them and their two daily cups.

I'm not satisfied with this ambiguity though. Even more unsatisfying, something is awry with the way I make coffee these days. I (as usual) use a cone filter, ground espresso from the CoOp and have not noticeably changed the recipe – but it just is not tasting the same. Every morning tea is looking a little bit better, though I've been hesitating to trust it to get the job done. All this makes it imperative for me to know: cutting through the crap, is coffee good for you or is it bad for you?

But, as a deviation before I get in to that, I found a wonderful legend about coffee’s origins cultivation from National Geographic's Web site. It goes along these lines:

“Goats will eat anything. Just ask Kaldi the legendary Ethiopian goatherd. Kaldi, the story goes, noticed his herd dancing from one coffee shrub to another, grazing on the cherry-red berries containing the beans. He copped a few himself and was soon frolicking with his flock.

“Witnessing Kaldi’s goatly gambol, a monk plucked berries for his brothers. That night they were uncannily alert to divine inspiration.”

Alright, back to the science. Here is what I found:

According to the National Coffee Association’s Coffee Science Source (CoffeeScience.org) coffee seems to reduce the risk of Type 2 Diabetes, Alzheimer’s and Parkinson’s. There is some evidence that it can improve physical performance when exercising (types the girl who is meant to be training for a half marathon) and protects against heart disease and cirrhosis of the liver. Coffee’s fiber and antioxidants help keep our colons and DNA young.

The articles warning against coffee seem to be slightly more of the “paranoid wing-nut” variety. They mainly point out the dangers of adrenal exhaustion, psychological dependences and “dead caffeine” (as opposed to live caffeine in green tea – give me a break).

So . . . my coffee problem seems mainly to be that I need to invest in a better coffee maker!

Further reading:
Coffee as a Health Drink? Studies Find Some Benefits (August 15, 2006, NY Times)

An afternoon at the Opera

State Opera House
Originally uploaded by danielle512

Sunday afternoon I saw the State Opera's performance of Puccini's Turandot. The State Opera house is a lovely little building near the National Museum. It's not as sumptuous as the Paris Garnier or San Francisco War Memorial (I've not been to so many others), but it has a sincere prettiness that is immensely appealing. The chairs could be a bit more comfortable though. 

Czech people are serious about dressing up, so I did by best to turn up turned out: heeled leather boots, black sheath dress, fuzzy turtleneck sweater (more in the interests of warmth than style), a tailored tweed jacket, dangly earrings, eyeliner and, and, lipstick. The opera staff and audience members addressed me in Czech, which felt like a reward for my efforts. (One of my definitions of successful travel is being addressed in the local language.)

Upstairs in the hallways hung portraits of notable performers associated with the opera house. By far the best was a delicious picture of Marina Vyskvorkina. She is shown, full locks flowing, oozing with scarcely containable fabulousness. I look at this photograph and think, “How cool must it be to be her?”

The performance began dull enough, but improved as the death toll rose. The most enjoyable singers were the comical Ping, Pang and Pong. These over-wrought ministers flitted around the stage like over-plumed birds in multi-layered be-sequened, be-tasseled headdresses, coquettishly fluttering fans in their hands.

At least one audience member did tear up at the show-shopping aria Nessun Dorma (click here to listen to a recording). Equally touching, though, was the crowd who came. Many large family groups: everyone from grandma to toddling little boy.

During one of the intermissions, I snapped a shot of a father instructing his young daughter: on his knees, sharing points from the program to an attentive audience of one.

Pretty in Prague

Volunteering for a better world: harnessing technology and willing citizens

(From this week's iSGTW)

By using the strengths of distributed computing technologies, both specialized researchers and citizens have the opportunity to participate in a new way of doing science.

We live in a time when nearly all information is available to nearly all people everywhere.

We are entering an age where all types of people can also contribute to many types of information. A school bus driver in rural Romania may be part of a biomedical research project. Or a banker in Los Angeles might moonlight as a collaborator in an astronomy project – classifying galaxies in her spare time.

This new movement in science, called “citizen science,” allows non-specialist volunteers to participate in global research. The projects are as diverse as backyard insect counts (the Firefly citizen science project), studies of how malaria develops and is transmitted (MalariaControl.net) or prime numbers searches (through PrimeGrid).

The marriage of distributed computing techniques with citizen science represents a potential revolution. It gives scientists access to more resources and makes “cybercitizens” participants in the research process. With a few mouse clicks and 20 minutes to spare a person can elect to aid scores of projects. They can aid as many or as few projects as they like, and their involvement does not damage the performance of their own computer.

Considering the average desktop is idle about 80% of the time, its spare computing cycles represent a large resource. After downloading the needed software, a computer’s spare analytical power is harvested to work on small pieces of a large problem that has been sent from the project’s server. Once completed, the results are sent back to the project. By sharing out large tasks to many computers a distributed “grid” of computers can reduce the time needed to solve complicated problems.

Where to Start?

[Read more]

Tenacious D and the Joy of Life

So, for anyone keeping track (are you there Mom?) I did indeed submit my application for grad school and have only now to wait. I am so sick with anticipation-slash-anxiety that I wish I could sleep for the next month and a half until the answer arrives.

I consider my chances of acceptance to be about 50-50 (either it could happen or it could not happen, right? For those who don’t have the time, just watch between 2:35 and 3:30 of this video. It’s worth it.)

I have already begun start thinking of back up plans. Perhaps I should make a go of freelancing as I am? Perhaps I should go to Haiti and volunteer in the rebuilding efforts for a year? What I really enjoy is reading, hiking and eating; any way I could finance myself next year doing that?

Shall I reapply for the following year? It was only on the third application that Fermilab accepted me as a science writing intern. For this determination a friend sweetly dubbed me ‘Tenacious D,’ an appellation I’ve held to me heart as a compliment ever since. An editor at Fermilab told me I held one of the most productive, successful internships in several years, so I may not completely be a lost cause even if I don’t get what I want at first.

On to the joy of life

Now, in other and possibly more important news, let me tell you about my musings over dinner last night.

Could it be that the point of life is enjoyable eating?

Let’s examine this from a couple perspectives. A biologist will tell you that the purpose of life is to reproduce and see your genes continued past your life in to the next generation. But for what? So that these life forms will feed and nourish themselves and pass your (and now their) genes on to the generation after that.

A spiritual person will tell you that the point of life is to cultivate devotion. To what end? So that you enjoy divine approval as you embody Ecclesiastes 3:12-13:

“I know that there is nothing better for men than to be happy and do good while they live. That everyone may eat and drink, and find satisfaction in all his toil—this is the gift of God.”

A person focused on nutrition and fitness might say that enjoying your healthy body is the point. But for what? To feel great throughout your long life while eating. A person who can extend their lifespan by 15 years through a healthy lifestyle gets to enjoy an extra 16,425 meals. 16,434 if those years include leap years.

Once I was done with my near-rapturous dinner of steak with pepper, shallot, estragon and Cabernet Sauvignon sauce, seared red cabbage and a glass of said excellent Cabernet Sauvignon, finished with a ramekin of lemon sorbet, vodka and red berries, I did return to earth. Having let the food intoxication pass, I think a satisfying life is built from a balance of intellectual-artistic (same thing really), physical and soulful pleasures.

On this note, I highly recommend affording yourself the 18 minutes to view Elizabeth Gilbert’s talk on nurturing creativity given at a 2009 TED conference. It is brilliant, humanistic and hilarious. Hearing her thoughts on genius and the process of creating art was possibly the most satisfying experience of my week – though dinner last night makes a very close second.

Answering a truly big question: How did dinosaurs move?

(From this week's iSGTW)

In a memorable scene from Steven Spielberg’s Jurassic Park, a Tyrannosaurus rex gallops behind a jeep, close to overtaking it, lunging to take a bite out of Jeff Goldblum — to the horrorified delight of millions of thrill-seeking movie-goers.

Assuming dinosaurs could be resurrected, how realistic would this situation be?

Not very, according to Karl Bates, a researcher in dinosaur locomotion. In fact, our scrawny-armed, prehistoric friend would probably have trouble outrunning a bicyclist. Depending on how fast you run, you may or may not be in trouble if you were on foot.

How does Bates know this?

Because he is a member of the Animal Simulation Laboratory at the University of Manchester, UK, which for over five years has made computer models of prehistoric animals to solve questions about how they moved and what they were capable of doing. This work helps answer how novel structures could help or affect animals, how different walking styles evolved, and how you get from a T-Rex to a modern bird.

Large predatory dinosaurs are his forte, especially the therapods (“beast-foot” dinosaurs believed to be in the lineage of modern birds). For his doctoral thesis, he chose to look into Acrocanthosaurus atokensis. “It is essentially the same size as a T-Rex and looks superficially similar but with big spines along its back,” he said.

It lived 110 million years ago in North America; its fossils have been found in Texas and Oklahoma.

“I picked this dinosaur because it is big, and there are fossil tracks and foot prints that are supposed to be from this dinosaur,” says Bates. “The proportions of its limbs are some of those most different from modern birds: very long thigh and short ankle bones compared with the short thigh and long ankle bones of birds. With these differences, how they would move is a very interesting question.”

Read the full story.

The problem with Geneva

I may have put my finger on the problem with Geneva. It’s a matter of mass and creativity. The place is not massively creative (unless you’re particular gig is, say, theoretical physics. Then it is Valhalla).

Now, don’t get me wrong. Geneva is fantastic in many ways. Good nearby mountains, good Italian restaurants, a good transport system. It also is pretty, and good looks can cover a multitude of sins. But there is a “critical mass ” lack in the creativity department. Let me expand.

This weekend a local music venue is going to be hosting a tribute night to Johnny Cash, Hank Williams and Dolly Parton. Now this is a wonderful idea! These are all excellent artists who did much to contribute to good country music in America (what little of it there is). Beyond that they all have distinctive attributes that would make them fun to imitate or “tribute”. Cash’s deep bass, for example, Williams’s hat, and as for Parton’s talents and endowments, they are, well, just too grand to mention.

However I sent out an invitation to the usual suspects, trying to drum up some enthusiasm for going. For at least seeing if it was interesting and what did I hear in reply? Not. A. Peep. Save for the odd, “Uh, thanks but I’ll pass.”

This is not a problem with my friend base, I believe, as much as it is a problem with my current city. My friends are quite nice and generally up for good times. However if I were living in San Francisco (closer to home), or near Chicago, New York or Boston I’m willing to bet the response from my friend base would louder and more enthusiastic. This is probably because a Cash-Williams-Parton tribute night would be really excellent in those cities, whereas in Geneva? I’m dubious. (I guess we’ll have to wait till Saturday to see.)

This sets us up, however, for a self-fulfilling prophecy. A city who does not believe it can have an amazing Legends of Country tribute night will never have said LoC tribute night. And that, my friends, is a shame for all of us.

Musings on persistence

It's mighty hard to be productive, isn't it? I should be working on my application to graduate school, yet I'd rather do almost anything else. Nearly anything. Except perhaps put away the remainder of the grocers that still need to be cleared from the kitchen after this weekend. Or finish washing the dishes in the sink. Starting new projects is much more fun than finishing them, in the way that making a mess is more fun than cleaning it up.

But I suppose nothing that is worthwhile is easy. And I suppose that it is through persistence that things are acomplished. How many times (in my memory alone) has the LHC been in for repairs? It's now running like a treat, but that is only thanks to tenacity.

I was thinking the other day that I would truly like to say “no” to mediocrity, but (if I really face it) I'm a mediocre long-distance runner, a mediocre snowboarder, a worse-than-mediocre guitar player and as for my writing, let's face it I'm not going to win the Nobel prize for literature anytime soon.

So I reckon the only thing for it is to a.) accept that for the moment my abilities in many areas are decidely average and b.) work, work, work to improve. If I think grad school is a key step in that then I guess I ought to take a bite out of the task that would possibly grant me access. Fine then, here we go.

The LHC Computing Grid in the starting blocks

Talking with Ian Bird, from the CERN Bulletin.

As the Large Hadron Collider ramps up operations and breaks world records, it is an exciting time for everyone at CERN. To get the computing perspective, the Bulletin this week caught up with Ian Bird, leader of the Worldwide LHC Computing Grid (WLCG). He is confident that everything is ready for the first data.

The Worldwide LHC Computing Grid (WLCG) collaboration has been in place since 2001 and for the past several years it has continually run the workloads for the experiments as part of their preparations for LHC data taking. So far, the numerous and massive simulations of the full chain of reconstruction and analysis software could only be carried out using Monte Carlo simulated data. Now, for the first time, the system is starting to work with real data and with many simultaneous users accessing them from all around the world.


“During the 2009 large-scale computing challenge (STEP’09), several major milestones were achieved: first the data transfer rates sustained were well above what was actually designed for – we achieved sustained aggregate data rates close to 4 GB/s – more than twice that required. This is equivalent to transferring a DVD of information every second. Secondly, the Tier 1 sites were able to show that they could accept this data stream, archive it on tape and simultaneously recall data for processing – all at the rates required during full scale LHC running, and in many cases well in excess of that rate. Finally, but perhaps more significantly, the experiments were able to demonstrate that the system could support large numbers of users running ‘real’ physics analyses on the data”, says Ian Bird.

Of course, the experiments have actually been collecting real data from cosmic rays for the past several months (not to mention some real collision data in the last weeks!) and have been putting the entire grid system through its paces so as to align and calibrate their detectors in preparation for full-scale data taking. ”Not only do we believe the system is ready, but it is actually in daily use already!”, confirms Bird.

Despite all possible simulations and tests that can be performed, no system can be fully understood until it is in use for real. “Undoubtedly there will be surprises when we start handling real data and we have to be ready to react and adapt to those situations. While in 2009 great steps were made in supporting many more users than just the experts, we still have a long way to go. This will no doubt be one of the areas where we have to be ready to adapt and improve things. There are several developments in hand that should help in this area and deploying those will happen this year”, assures Ian Bird.

During the past several years WLCG has made use of several grid infrastructure projects, including EGEE in Europe and OSG in the USA. Now, the landscape of European Grids is changing because the EGEE will come to an end in April 2010 and a new structure based on National Grid Infrastructures with European level coordination will be put in place. “This is potentially a major change in the underlying support structures for WLCG and, of course, the timing of this – just as the LHC physics programme takes off – is unfortunate”, admits Ian Bird. “However, that is the way it is and we have to focus on making this transition as smooth as possible”.

At the time when such a big project reaches this phase, the feelings of people who have built it must be of real anticipation. “Certainly not all of the grand ideas that had been discussed have come to fruition, but on the other hand today we really do already support data rates and workloads well in excess of those originally planned”, says Ian Bird. “The worldwide collaboration in computing that we have built in WLCG is really a first and I think we can all be proud of that – this surely will serve as a model for other international science communities that are on the horizon that will eventually produce data in amounts that will dwarf what LHC will produce, but we did it first! But now it really is time to put this to the test with real data ...”