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?

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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 ...”