Recent Muse-ings

Muse Last Night

Last night Muse brought its hard pop-rock to Lyon, France and I found myself part of the audience. The light show was impressive, the boys admittedly can play their instruments well and Matthew Bellamy's vocals are excellent live.

While the crowed whipped itself in to the expected frenzy, I couldn't help feeling like we were at a well-planned CD listening party. Save from a drum and guitar solo, they played their crowd-pleasing tunes essentially as recorded, infusing scant fresh emotion. It gave one the impression of being stranded on the moon.

Fresh perspectives for a better world

While it’s no surprise that technology has the ability to change the world, it sometimes changes it in surprising ways. The Citizen Cyberscience Centre project, is promoting change for humanitarian causes through distributed volunteer initiatives, such as volunteer computing and ‘volunteer thinking’. The inaugural lecture of a planned series was held in late October at CERN.

The United Nations Institute for Training and Research (UNITAR), the University of Geneva, (UNIGE) and CERN recently set up a new partnership and launched a lecture series, which will invite experts in the humanities and technologies to share fresh perspectives on ways to work for a better world. The inaugural lecture at CERN hosted two speakers, Mo Ibrahim and Alpheus Bingham, each of them behind initiatives using technology to address difficult problems.

Mo Ibrahim founded Celtel International, one of Africa’s most successful mobile network operators. Ibrahim’s company dramatically changed society in Africa – allowing millions of citizens to connect wirelessly, and thus promoting economic growth and social freedom. A study released this year by the World Bank found that a 10% increase in mobile-phone usage in developing countries increases GDP per person by 0.8%. The same study also linked a 10% increase in high-speed Internet connections with an economic growth of 1.3%. (A readable summary of this study can be found in this article in The Economist.) Citizens, for example, can avoid being swindled by checking market prices in neighbouring towns before agreeing to buy or sell goods. Self-employed workers can make calls to advertise their services. Money can be transferred remotely with mobile phones in Africa – making banking transactions and travelling more safe.

Perhaps more unexpectedly, technology is also promoting democracy in Africa. Mobile phones help observers monitor the outcome of elections – making fraud easier to spot. They are also used to report human-rights violations or to coordinate conservation projects.

Having sold his company for $3.4 billion in 2004, Ibrahim, along with his daughter Hadeel, is now behind a humanitarian foundation that supports good leaders in Africa by awarding prizes. He also uses his influence to promote business activities in Africa, believing that the continent is not only ripe with opportunities, but that it is also what is best for Africans. “I don’t believe in charities,” he says. “I believe in business. People should do clean business and that will do the job.”

The second invited speaker was Alpheus Bingham, founder of InnoCentive, a Web-based community that has shown a way to make it easier to connect difficult problems with novel solutions. Through its website InnoCentive puts “Seeker organizations”, who have a problem they are seeking a solution for, in contact with “Solvers,” who can win cash for offering the best solution.

Bingham’s belief is that, in many instances, outsiders (often in a loosely-related field) manage to bring fresh perspectives and innovative solutions to problems that have stumped “experts.” “InnoCentive harnesses the global reach of the Internet to let “Seekers” find the right “Solvers”, he explains.

“We hope the lecture series will focus attention on the broader aims of the Centre,” says Ben Segal, Citizen Cyberscience Centre collaborator, “of supporting development and education by harnessing the power of volunteer thinking and volunteer computing technology.”

This centre will help regional authorities, humanitarian workers and scientists harness the computers and the minds of volunteers on the Web, to help predict the impact of new vaccines for neglected diseases, study the effects of climate change on developing regions, or turn satellite images into useful maps of remote regions – to cite just a few examples of what citizen cyberscience projects are already doing today.

Thoughts from the dental chair

Best things about living in Modern Times:

1) Air travel – hit its stride in the 1930s. But honestly, who would have thought that we could sit in a chair, sipping a cup of coffee and be in a different part of the world in a few hours. Hear Louie C. K.'s thoughts as he speaks to Conan O'Brien about appreciating how good we have it today).

2) iPods – Launched ON THIS DAY (!) in 2001. You mean I can hear whatever song I want wherever and whenever? Wait, I get free Podcasts too?

3) Novocaine – discovered by Alfred Einhord, German chemist, 1905

It was this last invention I was particularly grateful for yesterday as I sat in the dentist chair trying to look on the bright side of things. The root canal was quite hard core – the jaw still aches. (I was even commended me for my patience -- a first coming from a dentist.)

How did people ever cope before? Dentistry used to be practiced by the people who cut your hair!

Who knows how they did it, but people have been getting by .... somehow. The first drills were allegedly "Bow Drills." Smaller versions of the bows popular with Boy Scouts trying to start a fire. Not a joke. After that people used all sorts of contraptions with wires, pliers, hooks, pins and other shudder-inducing implements. But for me it's the Novocaine that I'm a big fan of. In fact, I think the fear of old-style dental procedures would be the primary thing keeping me out of a time machine if I ever came across one.

I know I’m not the only one lately who has been seeing a lot of the dentist chair. As a few offerings:

How to Manage Dental Costs, With or Without Insurance: NY Times article about managing without dental coverage)

A Pictorial History of Dentistry: takes you from the Bow Drill to Cosmetic Dentistry

Guidelines about taking care of your teeth and gums: also from the NY Times – we know this stuff, we just need to follow it

Smells like ice

I am reconsidering my last posting. While my attempted ode to the glories of fall was done in sincerity, it has now turned really cold (unpleasantly so). Early in the morning the wind searches you out, finds a vulnerable spot and tunnels in. Tiny little icicles form in your blood stream and melt slowly over the rest of the day.

[Note: Thanks to FG for the photo, it captures the feeling beautifully.]

In adventures in baking: I did make the quinoa-apple-banana-chocolate bread last night. It turned out so-so. It is a little dense. I brought it in to the office, where it is enjoying some popularity. I think it might be worth another try someday.

Smells like Fall

Our thermometers and the angle of the sun in the sky have dropped lately. We are wrapping ourselves in scarves again and sunlight now has a golden sheen. Long distance runners are running the last of the year’s marathons. But what a great time of the year to jog! Any excuse to be out, gulping down gallons of purified autumn air, smelling like apples and wet grass.

I was thinking the other day about E. M. Forster. He might not agree with me. Of autumn smells he said that they are “odours of decay,” “pathetic” because they remind one of spring. However Forster was a depressive English man living in a depressing gray climate who wrote books about idealistic English girls traveling to sun-drenched places to be forever changed by an unexpected incident (okay, ‘sun-drenched’ in A Passage to India and ‘sun-kissed’ for his books in Italy. It seems that Tuscan weather is occasionally punctuated by powerful thunderstorms which stir passions and alter destinies.) However in Central Europe autumn has felt like a release, in the same way the harvest is the fulfillment of the growing season.

In addition to wear scarves and going for autumnal runs, I’m going to start baking -- so take that Forster. Project for the week:

Quinoa, banana and apple bread from La Tartine Gourmande (http://www.latartinegourmande.com/2009/09/25/quinoa-banana-bread/). Wish me well, and stop by for a bite if you’re in town.

Hawking report

Stephen Hawking spoke at CERN this afternoon in a sold out show. At least . . . it would have been sold out if tickets were available and I suppose it is actually more of a ‘colloquium’ than a ‘show.’

Anticipating a large crowd, my colleague and I arrived at 1:45 p.m. for a 3:30 talk and the auditorium was already nearly filled. I’m pleased also to say that the crowd was almost exclusively the 35 and under crowd. Amid these physics-loving, hipster types, with artfully disheveled hair the atmosphere was truly pre-concert: a few cold beers and Wilco-oozing speakers would not have been amiss. Folks were making themselves comfortable, swapping jokes, stories and snacks. I saw one girl with a large bag of kettle corn and a couple of lads splitting a bucket of pretzels.

This none-the-less being CERN people observations were peppered with statistics.

Guy on his mobile, “Dude you better get here soon, I’d say the seats are 75% filled.” One guy to another guy, “If these were benches instead of seats, 50% more people could probably sit in here.”

In this spirit we waited, the air in the room growing more and more stuffy, until Hawking entered. The room hushed reverently and there was much camera clicking.

Seeing him speak in person was a worthwhile experience, even if I was pretty much lost after the third slide of his presentation. (If you’d like to venture in to this territory, you can see a video of the presentation here.)

If you want the punch line of the presentation, I’ll distill it down for you: Standard Field Theory and Quantum Gravity lead to the spontaneous formation of universes.

He will also be giving a less-technical talk at the University of Geneva in a week's time—I might try to catch that too.

Battle cries!

I went swimming this weekend in our happy little Lake Geneva (more properly Lac Leman). There is nothing so unusual about that.

I also became convinced—not just once, but twice—that jumping off a platform five meters above the water (a little more than 16 feet) would be a good idea. This is rather more unusual. It sure was fun, but I could not hurl myself from the platform without releasing a primal scream of fear the whole way down. This has got me thinking, what is the link between fear, screaming and courage?

A little superficial Googling has turned up nothing of interest so I’m only going on my own (largely anecdotal, highly scientific) knowledge. It seems to me that our shouts and cries are meant to be advertisements that we are not afraid. We are after all drawing attention to ourselves. Perhaps this is also meant to disorient and frighten an enemy? Think of the marauding Berserkers, fierce Norse warriors who frightened the entrails out of people with their fearsome battle cries.

I bet anything that our “battle cries” (as mine certainly was when I was leaping off the platform in to the lake—I screamed so loud I have a sore throat) are more often than not a kind of bluff, a behaviour to make us temporarily feel braver than we believe ourselves to be. Just what the mechanism is for this I have no idea, but I bet it is there. And, as it got me off the tower and in to the lake, I’m grateful for it!

Improving Alzheimer's research a million scans at a time

New item in this week's iSGTW ....

Improving Alzheimer's research a million scans at a time

As you read this, your brain is busily working. In a complex but unconscious process, it scans the pixels on your screen, analyzes the images and turns them into meaningful information.

This week, a similar work began, neuGRID, that might help keep our minds whirring wonderfully as we (alas) age.

This massive scanning project will feed 6,300 magnetic resonance (MR) scans from more than 700 patients — a bit less than 200 images per patient, making for an impressive total of 1,260,000 images — through an automated series of calculations. This “pipeline” will analyze the cortical thickness of the brain (a measurement aligned with brain health) and its deterioration over time. The images are from the Alzheimer’s Disease Neuroimaging Initiative in the US, the largest public database of MR scans of patients with Alzheimer’s Disease and a lesser condition termed Mild Cognitive Impairment.

Feeding this entire database through these steps will allow neurological researchers to compare questions across populations, such as: What areas of the of the brain degenerate first? How relevant and accurate are the algorithms we use to model this disease? What morphological changes are disease markers? What drugs might halt or slow this disease?

Alzheimer’s is the second most feared disease associated with aging, following cancer, according to the Alzheimer Society of Canada. Patients with early symptoms have trouble remembering recent events, solving simple math problems, and remembering names of people and places. As the brain degenerates, patients in advanced stages of the disease lose mental and physical functions and need 24-hour care. Doctors do not know what causes Alzheimer’s. Although it affects about half of all people aged 85 and older, it is not considered part of the normal aging process.

neuGRID, a project funded by the European Commission, is analyzing the Alzheimer’s Disease Neuroimaging Initiative data set, squeezing the equivalent of five years of processing time on a single desktop into two weeks, to lay the foundation for much of their work in the future. This project is building a grid to support neuroscience research and hopes to become the flagship e-infrastructure for the community.

“Tweny years ago when I started in this field,” says Giovanni Frisoni, neuGRID partner and doctor who splits his time between reserach and patient care, “Alzheimer’s was equated with aging and regarded as a hopeless disease. Now we are starting to have the first medical treatments. This is an extremely exciting time to be in Alzheimer’s research.”

Application screenshot, showing the output of the CIVET pipeline - Human Cerebral Cortex. Darker areas indicate cortical thinning. Image courtesy neuGRID

Pooled resources

“This community has great computing needs,” says David Manset of Maat G, neuGRID services area leader. “These needs involve large data storage, fast access and massive processing for developing and testing new markers of disease — which grid technology can significantly help to address.”

The ability to evaluate disease markers — indicators of disease progression — will allow companies evaluate new drugs for treatment, speeding up the availability of new treatments to patients.

Computing clusters at three hospitals currently form the nodes of neuGRID’s infrastructure: Fatebenefratelli in Brescia, Italy, Karolinska Institutet in Stockholm, Sweden, and VU University Medical Center in Amsterdam, The Netherlands. Combined, their resources equal about 500 processing cores and 12 terabytes of storage capacity. Early next year, as the project moves into production, neuGRID hopes to access far more resources by joining with the Enabling Grids for E-sciencE “Biomed VO,” or biomedical virtual organization.

“I hope that in a few years we’ll be able to treat Alzheimer’s patients like we can treat hypertension patients,” says Frisoni. “With the correct drugs and care they can be essentially asymptomatic — showing no evidence of the disease.”

For many patients and their families, this would be a dream.

neuGRID will be showcasing this technology at EGEE’09. Don’t miss their live demo on Tuesday, 22 September at 4:30pm. They will demonstrate the real-time functionality of the infrastructure including data acquisition, algorithm execution and the advanced visualization output, accessible from an off-site desktop.

—Danielle Venton, EGEE. neuGRID will use the CIVET pipeline, developed at McGill University, Canada by Yasser Ad-Dab'bagh, et al. Learn more at neuGRID

Hiking: good for the body, more importantly good for the soul

Nicholas Kristof of the New York Times has been writing some good stuff lately of the joys of hiking, including a "how-to guide." My recent trip to the Alps reminded me of the pleasures of this simple, honest pursuit. If done right, you are left humbled, exhausted and inspired.

Here is a teaser from his piece "How to Recharge Your Soul":
"In short: Go take a hike! Backpacking is the cheapest of vacations, and it links you intimately and directly to the world around you. It reminds us that we are just a part of the natural order, not lord of it, and that humble acknowledgment is the first step to improve our stewardship.

Backpacking means you take on your shoulders everything you need to hike and camp. The key is to carry very little, say 10 pounds not including food and water. I frequently see tortured backpackers stumbling along as they lug gargantuan packs that dangle frying pans; in their torment, they gaze enviously at my small pack and mistake me for a day-hiker."

Read the full column.

What lies beneath . . .

Submerged beneath the waves lies a large part of human history.

For our ancestors, the ancient coastlines were attractive places to settle and experiment with what became the foundations of civilization. As the major glaciers melted between sixteen and six thousand years ago, these sites — where people first began to make fishing equipment, build boats and create permanent settlements — became engulfed by the rising seas.

But rather than destroying these ancient landscapes, the rising sea level instead preserved many of them, and with them many details in the story of our past.

“We have a lot to learn by looking under-water. There are many sites to discover and examine, and preservation is in fact often better than on land,” says Geoff Bailey, at the Department of Archaeology, University of York, UK. “There are large gaps in our general knowledge of early history.”

Read the full story in iSGTW.

The best thing ever: chocolate cherry yogurt à la Danielle Venton

In a first official 'sundries' post, I have to share with you my latest favorite discovery: chocolate cherry yogurt à la Danielle Venton.

Here's how you do it:
1. Take the Coop brand cherry yogurt.
(I guess step one would actually be 'get ye self to the Coop,' sorry should have told you sooner.)

2. Add a nice big spoonful of unsweetened cocoa powder.

3. Mix well and enjoy the most lovely, chocolate mousse-like cherry-tinged thing of goodness ever. It is probably not fair play to have this sort of thing for breakfast . . . yet it's what I did this morning, and I think tomorrow morning may call for a repeat!

If you try it, let me know what you think!

Bon weekend à tous!

Dragon Boating!

It is at least never boring around here. The Dragon Boat tournament in Dole was tons of fun . . . particularly because (or in spite of the fact that?) we won. No seriously. Out of 16 teams, even though we’d never rowed together before.

While we all appear happy in this victory photograph (below), I must admit that I was a little embarrassed. While we were all young-ish, hyper-competitive, athletic, over-achieving, darn-it-if-I-can-succeed-at-five-years-of-calculus-I-can-succeed-at-this-too, CERNois types (at least the other members of the team were), some of the teams we competed against were sweet, mixed-aged, mixed-ability cancer charities, with fewer members on their team. They had no chance. We were coached by one of the top kayakers in Britain (number 7 in a national competition—no joke), who kept us motivated by practice drills, inspiring speeches and loud shouting.

Our prize was several bottles of the vin jaune which is a specialty of the Jura . . . . feeling as I do about this kind of wine I couldn’t help but wonder, “This is an award?” Here we are on the celebratory stage to receive the honorary wine, I am the tall pale thing on the left with the water lily wedged in my hat and the dubious expression on my face.
More photos from this event (including quite a few of the rather muscular folks who operated the rudders) are here.

I kept trying to get people to sing the Trogdor from the very famous Sbemail58 . . . but my efforts were all in vain. Europeans! Sheesh!

It doesn't get much better than when it involves mammoth skulls

I'm working at the moment on one of the neatest stories I've come across in a long time, an archaeological project studying submerged prehistoric archaeology. (Read their news announcement.)

All I can say is if it involves mammoth skulls--I'm all for it!

In other water-related news I'll be paddling along with fellow CERNois at the Dragon Boat Festival in Dole tomorrow. Time to warm up the triceps . . .

Listening for whispers of dark matter

(Author's note: while I love working at CERN, my workspace is pretty standard . . . my office mates are all humans for example, some people have it a little more exciting. Digging this up from the old files . . . as found in symmetry magazine.)

Jodi Cooley works half a mile underground, in a mine that stopped operating 40 years ago. A rattling elevator takes her to work, 27 floors beneath the surface. The ride down the mineshaft is five minutes of complete darkness. A colony of bats inhabits the mine.

"For someone who's squeamish," says Cooley, "it's not the best work environment." When she is on shift she spends 10 hours a day in the mine, 10 days in a row. Looking to find a new type of particle, Cooley is listening for whispers of dark matter.

The underground experiment she works on, a collaboration of 60 physicists and engineers, is the world's most sensitive search for a type of particle that, as of yet, has only been theorized. The Cryogenic Dark Matter Search (CDMS) uses detectors chilled nearly to the lowest possible temperature, minus 273 degrees Celsius, to "listen" for vibrations caused by these particles streaming in from space. The discovery of these particles would revolutionize our view of the cosmos.

For Cooley, a postdoc at Stanford University, a day at the Soudan Underground Laboratory in Minnesota begins with a cup of coffee. After a telephone meeting with Dan Bauer, who leads the CDMS operations, she and her shift partner spend the rest of the day monitoring the experiment's cooling system, detectors, and electronics. Cooley, speaking from the mine by telephone, says she never suffers from boredom.

"Even when things are going smoothly, down here we can always find more work to do," she says. "There is no lack of work to be done."

Read the full article at symmetrymagazine.org.

--Danielle Venton

Better lasers on their way . . .

As Napoleon Dynamite as it might sound, we're en route to a world with better lasers thanks to MATLAB and grid comptuting . . . . (my article in the current International Science Grid this Week)

Do more with MATLAB

Researchers from disciplines as far apart as lasers and finance have a new computing tool at their fingertips: MATLAB can now run on Enabling Grids for E-sciencE (EGEE) computing power.

The software is a high-level language and interactive environment that enables users to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Widely regarded as a powerful piece of simulation software, for use in everything from optimizing rocket launch control settings to vector analysis, it is now fully compatible with any grid computing system using gLite middleware.

Read the full article here.

(Photo note: Using MATLAB on EGEE middleware, researchers can make a better laser - such as this solid state Cornellium Cn3+ laser created by a sapphire crystal. Image courtesy MATLAB Central)

Plenty more fish in the sea?

Article I wrote for the OMII-UK newsletter:

Once thought to be an endless source of bounty, rampant over-fishing around the globe has caused world fish stocks to plummet, with some of our favourite species hovering near collapse. The effects of over-fishing are being exacerbated by global climate change, which changes the distribution of species and the location of biodiversity hotspots. Under these conditions, good fisheries management is crucial. But how can stocks be controlled if we don’t know their location and numbers? A new grid-based tool, AquaMaps, looks like it could provide the answer.

Read the full article.

Starting a new blog -- very exciting

Welcome all, to the inaugural blog post of "Science and sundries."

I'll be a place for me to post updates about my latest projects and to-doings. Great to see you here!

Recent science-themed highlights in my life was the EGEE communications team meeting at CERN last week which involved a trip down the LHC pit to see CMS (the Compact Muon Solenoid detector). Easily the prettiest detector I've ever had the pleasure to see. See pictures from the work field trip here.