More microbe than mammal

I know I’m supposed to be in hibernation, but something came up that was so good I just had to share it with you.

You know by now that I am totally fascinated by the human microbiome, those trillions of microbes that make up most of the human organism. I’ve written here on Gydle about how microbes in our guts may implicated in a variety of ailments, from diabetes to Parkinson’s to obesity and irritable bowel disease.

I also wrote recently that the massive NIH-finded Human Microbiome Project has had a number of publications like this one in Nature Magazine that outline thier discoveries about the makeup and function of a “healthy” human microbiome.  I have a feeling that what we find out about the microbiome may well revolutionize our approach to health and medicine.

You might also remember from last year that I’m also fascinated by the concept of crowdsourcing, a kind of data gathering approach that takes information freely and painlessly from tons of people who are just going about their ordinary lives. They’re mined for data while driving, surfing the internet, ordering things online, logging into websites, reading wikipedia pages, looking at the stars, pooping… Continue reading

Weather bugs

I mentioned in an earlier post that I have a sneaking suspicion that we’re being crowdsourced by bacteria. Remember? The human body has 10 trillion cells in it. We also each harbor about 100 trillion microbes. There is more microbial DNA in the human body than human DNA. That post.

We know relatively little about this huge population, but one thing we do know is that it’s not random. I claimed, back in May 2011, that perhaps humans are not so much organisms as we are ecosystems.

We thought we were the top guns on this planet! We thought it was all about us! We thought our bodies were vehicles for our splendiferous brains! No, silly. We are being maintained. We exist simply as biomes for colonies of established bacteria. Our brains probably just evolved as the best way for our bacteria to ensure that they will continue to have thriving hosts, generation after generation.

You might have laughed that one off, and I can understand your reaction. It’s a little unsettling to think that humans aren’t the center of the universe. Galileo encountered a little resistance, too. I can be patient.

But why?  You might ask. Why would they want us to do their bidding? And what is their bidding?

Would it help you see my point of view if I told you that bacteria are controlling the weather, too?

Continue reading

Fold It!

As I stand in the Lausanne train station holding a sign saying “Marcel,” the volume of passengers from platform 8 dwindles from a steady flow to a trickle to a stop. He probably exited the other end of the platform. I stay put like you’re supposed to when you’re lost. He was the 20-something computer geek. I’d let him find me.

Sure enough, a few minutes later, he does. This amiable, t-shirt-clad student has come all the way from Zurich after his 8:00 class at ETH to show me how to play a protein folding game called FoldIt. The IT dude in my novel is a player, so I have to learn it, too.

In EPFL’s Rolex Learning Center a half hour later, we quickly download the game onto my Macbook, since his HP is bugging, and he logs into his account. A list of protein puzzles appears, with names like quick fix the loop puzzle, New Player Puzzle: Pollen Allergen Protein, Quick Flu Design Puzzle 3, Symmetric Foldon Puzzle 1. Underneath each puzzle is a brief description. Here’s one:

Foldon is a small, 27 residue domain from the C-terminus of a phage virus protein called fibritin. Your job is to fold 3 chains into a larger trimeric domain that includes foldon. You’ll be allowed to move foldon around as well, but you can only mutate the residues in the polyalanine extension. And remember, three-fold symmetry will be enforced! If you are new to Foldit, make sure you have completed Intro Puzzle 5-2, & 7-1 through 7-4. More details in the blog.

Holy crap, what am I getting into? I think. But Marcel dives right in and puts the flu design protein up on the screen. The backbone, he explains as he twists the protein around, is made of amino acids, arranged in macaroni-like helixes, flat sheets and sausagey loops. Poking out from it are key-like side chains, the blue ones hydrophilic, or water-loving, and orange ones hydrophobic.


He shows me how to zoom and twist the protein around, how to put purple rubber band-like things onto various arms of it and pull it together or stretch it apart, how to change a loop to a helix to a sheet, and how to freeze one bit and tweak another. Hydrogen bonds, which look like blue-and-white barbershop poles, like to form between sheets and along helixes, he explains, showing me how to line them up.

Angry red bombs appear when things get squashed too tightly together – clashes. Big, pulsing red blobs appear when there’s too much empty space – voids. You want to avoid those. We fiddle with the side chains, rotating the orange ones in and the blue ones out. He even shows me how to “mutate” them.

The whole time, he’s keeping one eye on the score that’s evolving in the upper part of the screen. He makes a move that results in a huge loss of points; our score plunges into the negative numbers, turns red, and lots of red bombs appear. “Quick! Put it back!” I panic.

“Hang on,” he laughs. He’s totally relaxed. “Now we’re going to wiggle and shake.” He clicks a button and the whole structure starts bouncing, complete with a ticking soundtrack in the background. I watch as the points move rapidly upwards out of the red, then gradually slow down, while still increasing. After a while, Marcel clicks the wiggle off. Our total is higher than it was before!  Then he clicks another button and all the side chains start rotating. Once again, the score ticks upwards. We sit back, satisfied.

The points represent energy, he explains. The native structure of the protein is going to be its lowest energy state. The higher the number of points, the lower the energy state. But like a ball on a golf course, you can get stuck in a local minimum and miss the hole you’re shooting for. “It’s like this building,” he says, looking at the undulating floor of the Learning Center. “A ball will roll down into a hole. But that doesn’t mean it’s the lowest hole around. It’s just the one it was nearest.” Sometimes you have to pull back quite a ways and shake things up to get the ball to roll into a deeper hole – a lower energy state.

When a protein is manufactured in the cell, it zips into this native shape in no time flat. The shape is critical to the protein’s function. Sometimes, if the environment isn’t right or there’s a problem with an accompanying protein, called a chaperone, the folding doesn’t go right. Misfolded proteins are implicated in a variety of diseases like mad cow, Alzheimer’s, Parkinson’s and cystic fibrosis.

Scientists would dearly like to be able to predict the structure of proteins, because then they could design drugs that could fix the misfolded ones, or disable the harmful ones in viruses or bacteria. With this kind of knowledge, perhaps some day new proteins could be engineered for gene therapy or other medical miracles.

Algorithms to predict structure chug along on huge servers or in distributed computing networks, like rosetta@home, which uses spare CPU on home computers to run its calculations, but they take forever because they have to brute force every conceivable possible convolution. There’s no guarantee the algorithm will find the lowest energy state, either, even after all that calculating. It’s a really complicated problem. FoldIt taps into something these algorithms cannot – human intuition and pattern-finding capabilities.

Marcel shows me the different puzzles available – they range in difficulty from easy structures put up for newbies like me to complex proteins involved in actual scientific research. There are only a few on at a time, each one with an open window of about a week, in which players work either on their own or in teams to get the highest possible points before it “closes.” You can “evolve” a protein, which means you work on a solution, and then share it with other people, who then add their bit to it, and so on. The protein’s structure then progresses as a joint effort. You have two rankings – “solo” and “team,” based on your results in each category. Marcel is a member of the Androids team.

He estimates that there are about 300 really active players, spread all over the world. The master solo player is a guy from Slovenia called Wudoo.  A woman in Texas with a couple of kids, jpilkington, is the “evolver queen,” he tells me in reverent tones. While we’re playing, she comes online and starts chatting with other players. I tell her my brain is exploding. “LOL,” she replies.

Rav3n_pl, a programmer who lives in Poland, is a master at writing “scripts” –recipes that apply long strings of commands to the protein, which can be run in the background for hours while you’re off doing something else. Marcel started the flu design puzzle that morning. He first did a few manual tweaks, and then ran one of Rav3n_pl’s genetic algorithm scripts while he took a shower and ate breakfast. “The manual stuff can only take you so far,” he explains. After that, you eke out points at a time by running scripts. (These recipes, BTW, are the subject of a recent article in PNAS.)

As we continue to work the protein, I see what he means. The score appears to be stuck. “The deeper you are in an energy hole, the harder it is to move something,” he says.  He opens the “cookbook” he has set up on the left hand side of the window and starts a script. We watch the protein jiggle and shake, the points fluctuating wildly as it starts, stops, reverts and starts another iteration.

Finding your way out of the hole is an art. There are a few people who are consistently among the top scorers, he tells me. “It’s not just luck. There’s something – either they have an intuitive feel for how the programming works, or they see patterns, or maybe they just have good computers and can run tons of scripts.”

Marcel has been away for a couple of weeks on military duty. Even so, his overall rank is 61. Wow, I say, you must play all the time!

“No, not more than an hour or two a day, max,” he assures me. “And a lot of that is just scripts running.” He admits, though, that when a deadline is approaching, he might put more time in with his team.

Well, sure, but you must also know a ton about molecular biology, in order to be able to rack up a ranking that high?

“Nope,” he says. “I just like getting the points. Sometimes you make a move, and you get a few points, and the protein just looks right, and it’s an amazing feeling.”

He also likes the social aspect of the game. “I’d never just play it offline,” he says. “I like chatting with my teammates. What should be the next step? What’s going on in their lives?” True. He is a chatty guy. He’s spending the entire afternoon with me, an uber-noob novelist, after all.

I figure he got into the game because he’s a chemistry student. “Not really,” he tells me. “At first, I looked into the seti@home thing, but then, really, who cares about aliens? I found rosetta@home, and that was cool, proteins are important, and it was there that I found out about FoldIt.”

Finally, we open the most recent puzzle on the site, something called a CASP roll, a “freestyle” protein with 197 amino acids that has to be folded from scratch. Sometime in February, the best FoldIt solutions will be compared with solutions cranked out by algorithms running on servers and with experimental data from x-ray crystallography and nuclear magnetic resonance imaging.

“Just look at that!” Marcel says as we contemplate the unfolded backbone stretching off into the screen. “197 amino acids! It’s huge!”

The CASPs are cutting edge science. A previous CASP puzzle solved by FoldIt gamers was published in Nature in September. Researchers had been struggling with an enzyme in a monkey version of the HIV virus. Despite the existence of several crystal forms of the protein, they were unable to solve its structure computationally, even though they’d been working on it for a decade. But if they could figure out its structure, they could engineer a way to disable it, thus hobbling the virus. They posed it as a FoldIt challenge, and within three weeks, two teams of FoldIt players (the Contenders and the Void Crushers) came up with multiple possibilities for its structure, enabling the scientists to further refine the game, which in turn led to the discovery of several molecular targets on the structure that can now be used to develop retroviral drugs.

As I drove Marcel back to the train station later that afternoon, I felt a little guilty. He’d spent his whole afternoon playing FoldIt with me, and his score hadn’t moved a whole lot. But then I remembered he had a two-hour train ride to Zurich, and a USB internet key.

About that gut feeling

More news on the microbiome. As I explained in my post about bacterial crowdsourcing, each and every one of us hosts about 100 trillion microbes in and on our bodies. This population is known as the “human microbiome.” They’re everywhere – armpits, butt cracks, skin, nostrils… and guts. Our guts alone harbor more than 1000 different kinds of bacteria.

The microbiome is a very hot area of research right now, and rightly so, in my opinion. The US National Institutes of Health is pouring money into the Human Microbiome Project in much the same way they funded the Human Genome Project starting in 1990. Understanding our own cells isn’t enough, see, cuz guess what? All those critters probably aren’t just sitting there doing nothing.

Recent research bears this out. A team from University College Cork recently reported on research in which they fed mice probiotic bacteria for six weeks and then observed their behavior.  The mice receiving the probiotics exhibited fewer signs of stress and anxiety. They spent more time exploring nerve-wracking places like elevated walkways and had a smaller spike in their stress hormones when placed in water, another really scary mouse experience. Lead researcher John Cryan was psyched:

“This was really exciting because it tells us the animals are more chilled out and don’t mount the same stress response.”

Even more interesting is that when the researchers cut the vagus nerve (which connects the nerve cells in the gut with the brain), all these beneficial effects vanished. The probiotics aren’t affecting the brain chemistry directly, they’re affecting the gut chemistry, which then gets transmitted somehow to the brain.

Jonah Lehrer wrote about the research in the WSJ, “The Yogurt Made Me Do It.” He proved once again why he’s my all-time favorite science writer by focusing on the study’s philosophical implications. Most of us “feel” like our minds are different than our bodies. But if we extrapolate from that mouse study and assume the premise might also hold true with humans, then what we’ve got in our guts affects how we feel, and how we experience the world. You should really read the whole article, but here are a couple juicy snippets if you don’t have time:

There’s nothing metaphorical about “gut feelings,” for what happens in the gut really does influence what we feel.

This research shows that the immateriality of mind is a deep illusion. Although we feel like a disembodied soul, many feelings and choices are actually shaped by the microbes in our gut and the palpitations of our heart. Nietzsche was right: “There is more reason in your body than in your best wisdom.”

In another piece of recent research, scientists show that antibiotics can permanently destroy some species of our gut flora. Maryn McKenna writes about it in her Wired blog Superbug. We’ve evolved along with our microbiome in a lovely symbiotic adaptation that’s gone on over countless millenia. Are we eradicating all that hard work in just two generations by flagrantly overtreating common, non-life-threatening infections?   Connect these two pieces of research and see what you get. Good gut bacteria = good mental health. Antibiotics kill gut bacteria permanently. Depressed, anyone? Stressed? My question: can yogurt offset this? Are my children going to spend years in therapy or pop Prozac for the rest of their lives because of all that pink antibiotic they swallowed when they were babies? Is the whole thing just a Big Pharma Plot?

As I dug through these fascinating bits of evidence of the microbiome’s importance in human health, I ran across yet another connection. Last June, NewScientist magazine reported on research that found that autistic children had a different “gut bacteria signature” in their urine than normal children.

“It adds another link to the gut bacterial involvement in the onset of disorder,” says Glenn Gibson of the University of Reading, UK, who has previously identified abnormally high levels of clostridium bacteria in children with autism.

One possibility is that the gut bacteria in children with autism are producing toxins that might interfere with brain development. One of the compounds identified in the urine of autistic children was N-methyl-nicotinamide (NMND), which has also been implicated in Parkinson’s disease.

They were hopeful that this could be used as a sort of diagnostic tool, in the hope that addressing the problem earlier, even before behavioral traits showed up, would be beneficial. I hope they go further than this, and try and figure out a way to restore the health or these kids’ gut microbiomes, rather than just help them cope with the effects of toxic ones.

All this research illustrates that the gut microbiome plays a critical role in far more than just our gastrointestinal health.  I already wrote about the possibility that the microbiome very likely plays a role in cancer. It’s a good thing that we’re broadening scientific inquiry beyond the limited scope of the human genome. There’s a whole lot more in our navels (and our breakfasts) that merits a good, long gaze.


Looks like I spoke too soon with all my good news. That same day, right after I finished the post, I got two slamdunks. One, a massive forest fire is threatening my hometown of Los Alamos, New Mexico, and two, my brother (the one that’s not a geek, or rather, not quite as much of a geek. We’re all geeks because we were raised in Los Alamos) was in a car accident in Montana. Thankfully, he’s fine. But the fire is not. It has burned over 60,000 acres so far and as of last night, was zero percent contained. The town’s best kept secret, its awesome ski hill, is starting to burn. It’s horrible and dangerous and devastating.

UPDATE: as of 5 hours ago, it’s now 3% contained. Current info is available here.

This morning, I did the usual. Early morning chat with my newly-appointed CTO, aka my brother Dave.

Dave: Hey, Mary! Did you see Los Alamos made Drudge?

Me: No!

I go check it out. There have been a lot of forest fires in the southwest US this summer. What’s different about this one? Why is it on Drudge? The answer is in the red, all-caps title: NUKE LAB FIRE DANGER

It continues in the first paragraph from the AP release:

A wildfire near the desert birthplace of the atomic bomb advanced on the Los Alamos laboratory and thousands of outdoor drums of plutonium-contaminated waste Tuesday as authorities stepped up efforts to protect the site and monitor the air for radiation.


Got your attention yet? Good grief. Might as well just post a picture of a big, red PANIC button. Here’s a similar one from Reuters:

The fire’s leading edge burned to within a few miles (kilometres) of a dump site where some 20,000 barrels of plutonium-contaminated waste is stored at the Los Alamos National Laboratory, fire officials said.

Yes, there are drums containing low-level nuclear waste in Los Alamos. Nuclear weapons research does happen there. Plutonium, a by-product, exists. It’s radioactive. But a “dump site”? The immediate conclusion drawn by Joni Arends, executive director of the Concerned Citizens for Nuclear Safety, is (drum roll, please) that “these drums will get so hot that they’ll burst .. and put the toxic material into the plume” strikes me as just a tad alarmist. Yes, I’m being sarcastic.

The DOE may be incompetent, that’s up for debate. But they’re not totally irresponsible. They’re not going to store this stuff in barrels that can explode. This area is known for its fire danger. After the 2000 Cerro Grande fire, which destroyed hundreds of houses in the town, “additional measures were taken” to ensure that things were safe in the event that history repeated itself. Los Alamos is many things, I’m not going to go into that, but I really don’t get the impression that they have a laxist attitude about radioactive material. Quite the contrary.

Joni goes on to worry about how the fire is going to “stir up contaminated soil” where experiments were conducted years ago. “Burrowing animals have brought that contamination to the surface,” she said.

So she’s not just an expert in nuclear waste containment vessels, but animal behavior as well! Way I look at it, if the fire does get to the lab, it’ll flush out all those burrowing varmints and solve that problem but good.

Despite the mandatory evacuation order, a few hardy souls stayed behind. When asked if he was worried about the flames reaching sensitive materials, chemical engineer Mark Smith said “the risk of exposure is so small. I wouldn’t sit here and inhale plutonium. I may be crazy, but I’m not dumb.”  No, he’s not dumb. Nobody who works at Los Alamos is on the “dumb” end of the IQ scale, trust me.

For more information on the situation, I’d recommend reading this cnet post by fellow Los Alamos native Stephen Shankland. He actually knows what he’s talking about.

Like Stephen, I’m also thousands of miles away, but I’ve been able to keep track of what’s going on thanks to another crazy guy I went to high school with. Joe had experienced the Cerro Grande fire and decided not to evacuate this time, because his house was on the eastern edge of town, farthest from the flames, and close to several exit routes. He’s been taking advantage of his days off from work to riff on his guitar and bicycle around town taking pictures. He posts them along with useful updates on his Facebook page.

Place is a ghost town. So… I hooked up the Marshall stack, cranked the stereo to 11, and played along to Rush and Zeppelin at full volume, just cranking the tube amp on my guitars. No neighbors to annoy. I’ll not get to do this again in a long while.

Even the locals are turning to Joe for their updates, because – surprise, surprise — the media isn’t terribly informative. One significant thing I learned from his pictures is that Los Alamos now has a Starbucks. When I was growing up the big excitement was daylight donuts, the bowling alley and the Big Cheese Pizza. If there had been a decent coffee shop back then I might have considered staying. Heck, I might have settled in, written a young adult novel and made millions like J.K. Rowling. Damn.

Somebody asked Joe if anyone had harassed him for not evacuating. “Not a word,” he said. He watered his neighbors’ day-lilies and fed the birds. He’s established a phone warning system with other die-hards, so if things get dicey while he’s sleeping he’ll be warned in time to get out.

Rain isn’t imminent, and winds are picking up, he posts. On another Facebook thread, people suggest diverting the excessive Utah snowpack or the flooding Mississippi via pipeline. Civil engineering is slow, though. But wait a minute. What if we could crowdsource it? Get thousands of people to go to home depot, buy a length of pipeline, connect it with their neighbors… only problem is that, unlike Switzerland, the southwest is covered by vast expanses of nothing but sagebrush and jackrabbits.
I’ll be in Santa Fe, neighbor to “the desert birthplace of the atomic bomb” next week and can breathe the fumes in person. I can’t bear to see it burn. It’s such a beautiful landscape, and even though I haven’t lived there since I left for college in 1983, and my parents moved to Santa Fe in 1990, it’s still the place where all my childhood memories reside. Sailing balsa boats in the Bandelier creek. Jumping off the high dive at Barranca pool. Making the 2-mile trek down Barranca hill on my bike in the summertime to buy candy at the Piggly Wiggly on Conoco Hill. Bombing a ski slope with friends, poles tucked under my arms. Running across a rattlesnake while rooting around in the canyon behind my house. Making out with my boyfriend on the edge of the mesa, totally taking for granted the stunning 100-mile view in the background…

Meanwhile, nearer home, as I was taking Luc to the train station this morning I noticed a plume of black smoke rising from a nearby apartment building. When I got back, fire trucks were in place and three little girls in their nighties were cavorting on the lawn of the parish hall across the street. They turned the event into an opportunity, of sorts.

Photo Credit (panic button): Krysten_N via Compfight cc

Crowdsourcing Babel

5277404580_1cd8923c02_mIn my second post on crowdsourcing, my brother Dave made this comment (spelling mistakes corrected): “You could become wealthy if you could figure out how to use crowdsourcing for translation.”

Well, it’s happening! I just found out today that a group led by CAPTCHA inventor and Carnegie Mellon prof Luis von Ahn is crowdsourcing people to translate stuff under the guise of an online language course called Duolingo. (After this I’ll stop posting on crowdsourcing. For a little while. I did say it was a big iceberg, didn’t I?)

Here’s how it will work. Say there’s a website in English that they want to translate into Spanish. They take the text from the website, break it down into sentences, and use these sentences as exercises in a free online English course for Spanish speakers.  A person taking the English course would read the sentence, and then enter what she thinks it means (in Spanish) on her computer. That’s effectively an English-to-Spanish translation. (I’m not sure it’s the best way to learn a language — but then that’s not their goal, is it?) If you get enough people to “translate” that same sentence, you can do either a statistical analysis to find the most common translation, or get people to vote on the best translation.

I hope they’re not planning to do translations the other way around — let the Spanish person do translations into English. One of the cardinal rules of translating is that you always translate into your mother tongue. You should never attempt to translate into a language you’re not totally fluent in. There are too many expressions, turns of phrase, and words that just don’t “go” together.

That brings up another potential hurdle; unlike the reCAPTCHA crowdsourcing (those squiggly words in boxes that prove you are a person and not a spam-monster), this one requires people to string words together into sentences. Just like gut bacteria, writing ability varies wildly from person to person. Just understanding separate words doesn’t mean you have a clue as to how they should go together.

So that means the clincher is going to be getting enough people involved to even out all the failed attempts. The language course will be free, which is a start. If on top of that it’s not fun and cute and motivating, it’ll tank for sure.

I have signed up for the Beta version. Initially, they will only be offering English, German and Spanish, the languages the developers know personally. (They’re not franco-phobic as far as I know.) I’ll be signing up for Spanish. I tried to learn German in order to help Luc get through 9th grade and my head almost exploded.

That brings up another question: why are there always beta versions? Why is it that we never get to sign up for an alpha version? Or is the alpha version the one that exists inside the inventor’s head?

And another question — how will they choose the texts to translate? To generate income, I can imagine they’d set up a translating business and then use this language course to do the work. But the texts might not all be that practical for the language learner. Tips for preventing Cholera. Machine tool specifications. The LL Bean catalog. Never mind. It’ll all come in handy sometime. You never know when you might be in need of a barn jacket. I’m not sure Dave was right, that you could get rich doing this, but I hope they do.

I hope I’ll be able to rack up points or something. That’s not quite as motivating as money or jelly bellies, but would be a better use of my time than trying to beat my high score in Scramble on Facebook. I might actually learn something in the process >Here’s a video of von Ahm talking about CAPTCHA and Duolingo at a TEDx conference at CMU:


Photo Credit: Alice Hutchinson via Compfight cc

(I think this cat has the right attitude…)

Crowdsourcing, Part III

Saturday I wrote a post about how I wasn’t aware of what was going on in my body, and how unsettling that felt. So unsettling, in fact, that I wasn’t able to write the post I had been planning for several days, and had to gaze intensely at my navel for a whole weekend instead.

That was probably a good thing, because it gave me some new insight into this post. Navel gazing isn’t all bad. Turns out there’s some pretty interesting stuff in there.

Last fall I translated an article by Daniel Saraga for Reflex Magazine about the gazillions of bacteria we have living on and in our bodies. The title (in English) was “Me, Myself and I – and a million other germs.” It should actually have been “Me, Myself and I  – and 100 trillion other germs.” Continue reading

Crowdsourcing part II

A few days ago, I wrote a post about smartphones and traffic jams.  Pretty soon, thanks to billions of anonymous bits of data flying all over the place, you won’t have to get stuck on the freeway or wait in line at Disneyland ever again. I have since learned that the smartphone stuff was just the tip of the crowdsourcing iceberg. Down below the penguins and their migratory traffic jams, the iceberg is gargantuan. It boggles the mind. We’re like the Titanic, most of us. Blissfully unaware.

Way back in 1999, UC Berkeley started tapping into the unused processing power of home computers all over the world to scan radio waves for evidence of extraterrestrial life. Currently, more than 3 million people are involved in the SETI@home project, doing their little bit to locate aliens. CERN also uses volunteer-based distributed computing to crunch its enormous particle physics data sets, a task that would constipate even the biggest, baddest supercomputer in the world. The rise of the internet has been nirvana-like for people in charge of iterative tasks like these that can be distributed, calculated remotely, and then reassembled into some meaningful form at the other end. All that computer power for free! You don’t have to put an expensive IBM petaflop supercomputer into your project budget, you just have to convince a lot of people (a crowd!) that volunteering the unused processing power on their PCs is a cool thing to do.

I could get my mind around this. The next step should have been obvious to me. But it happened so subtly it didn’t even register. Until my smartphone epiphany, that is.

Computers are great for a lot of things. Give a network of computers a number, an equation, a set of parameters, and they crunch away happily. A symbolic smorgasbord. A banquet of bits. A few more dimensions? Ten thousand more iterations? Not a problem. Computers don’t sleep, have sex, demand respect, drink coffee, or take sick leave. They won’t join a union, have babies or demand yearly pay increases. And when those computers all belong to other people, you don’t even have to pay for it. How great is that?

But unfortunately there are quite a few things computers can’t do very well. They can’t identify faces, emotions, words and images from partial or incomplete samples. They don’t get when something’s funny. They’re unable to recognize and capture beauty in music, art, dance or photography.

The human brain – even the most average, run-of-the-mill, McDonald’s eating, MTV-watching brain – can do things no computer on the planet can do, and all on the power of a 60-watt lightbulb. Such a terrible waste! All those brains out there, operating at a fraction of their potential. All that valuable processing power squandered on mundane tasks like navel gazing and Facebook.

What if you could find a way to connect all those brains, get them to communicate and interact without having to be in physical proximity? Get them to join a global network of some kind? Now that would be a truly formidable source of information processing, a machine that could handle just about any problem. Uh, wait a sec…

And that, my friends, is the essence of crowd-sourcing.

I have seen the future and it is the iceberg.

In case you still don’t get it, here are a few examples.

Wikipedia. The classic. Why hire a bunch of encyclopedia writers when the world is full of experts who will write copy for free? And in case they make mistakes, there are more experts out there to correct their copy for free? Wikipedia is a crowd of know-it-alls. And the information it contains is being constantly refined.

iStockphoto.  Why pay a photographer hundreds of dollars for the rights to use a photo when the world is full of excellent amateur photographers who would be ecstatic to sell their shots online for a dollar?

Citizen science. Why pay for those grad students when the world is full of geeks that will do your gruntwork for free? Identifying protein folding patterns was turned into a game called Foldit, in which volunteers outperform computers consistently. In Galaxy Zoo people look at images of outer space and classify the galaxies they see in them. You build up a “reputation” for how accurate you are. Several novel structures have been discovered this way, such as a “weird green thing” (Dave’s description) called Hanny’s Voorwerp. Herbaria@home taps into the British armchair naturalist crowd to document the vast numbers of plant specimens held in the UK’s herbaria. “Documenting large herbarium collections is an extremely labour-intensive task and most museum collections are woefully under-funded.” You get the picture.

Corporate R&D. Why pay for an expensive R&D department if you can avoid it? Companies like Boeing, DuPont, Procter & Gamble and Eli Lilly post their most intractable scientific problems on a website called InnoCentive, which anyone can join for a small fee. The companies (“seekers”) pay anywhere from $10,000 – $100,000 per solution. More than 30% of the problems have reportedly been cracked, “which is 30 percent more than would have been solved using a traditional, in-house approach,” said InnoCentive’s chief scientific officer Jill Panetta. And just think of all the money they’ve saved not having to shell out for health insurance benefits!

CAPTCHA. I like this one the most. Say it aloud. Isn’t it clever? It stands for Completely Automated Public Turing Test to Tell Computers and Humans Apart.  Whenever you are asked to type squiggly, hard-to-read words in order to verify that you are a human being and not an evil, webtrolling, spamming bot, you are solving a CAPTCHA. It turns out that a lot of the words in these images are from old documents that have been scanned for archiving. Computers parse the images, turning them into digital text, which takes up a lot less room. But often the computers can’t decipher the images. From the reCAPTCHA website:

About 200 million CAPTCHAs are solved by humans around the world every day. In each case, roughly ten seconds of human time are being spent. Individually, that’s not a lot of time, but in aggregate these little puzzles consume more than 150,000 hours of work each day. What if we could make positive use of this human effort? reCAPTCHA does exactly that by channeling the effort spent solving CAPTCHAs online into “reading” books.

When you are asked to solve a two-word CAPTCHA like the one in the picture, the first word is already known and the second word is one that a computer hasn’t been able to read. If you get the first one right, then they figure you’ve got the second one right, too. The image is sent out to lots of people to statistically verify that your answer is correct. I bet you didn’t know you were being crowd-sourced when you typed in those words. I sure didn’t.

Combine spam protection with 150,000 hours of free human optical recognition processing per day. That has got to be the ultimate win-win.

Crowdsourcing takes impossible tasks and turns them into games, contests, and time-fillers for millions of under-occupied neocortexes around the world. I once read an article about an eccentric genius who claimed he wanted to build “the game layer on top of the world.” I thought, “huh?” Now I think he might be onto something. Where is it written that we have to spend our waking hours doing things we think are boring and unsatisfying? Life’s a game. Join the crowd.

My brother Dave (who started all this) said, “You could become wealthy if you could figure out how to use crowdsoursing for tranbslation.”

“Or spelling,” I replied.

Crowd Pleasing

On a ride into San Francisco one day my brother pulls out his smartphone, hooks it into a cradle on the dashboard. So let’s check out the traffic on Google maps! Up pops the live traffic situation — the freeway is green if it’s smooth sailing, yellow if it’s slow and – 10 points if you can guess the color – if it’s stop-and-go.

How do they figure that out? Does the satellite look down, count the number of cars or their speed, judge the traffic flow, and upload the color? No, Dave tells me, it’s a clever app that takes advantage of the fact that most Californians have two things in common: they have GPS-enabled smartphones and they’re obsessed with avoiding traffic jams. Here’s an explanation of how it works from an official Google blog back in August 2009:

When you choose to enable Google Maps with My Location, your phone sends anonymous bits of data back to Google describing how fast you’re moving. When we combine your speed with the speed of other phones on the road, across thousands of phones moving around a city at any given time, we can get a pretty good picture of live traffic conditions.

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