10 reasons to get a good night’s sleep

Posted on March 16, 2012 by gydle

In celebration, I urge you all to drop everything and take a nap.

As I mentioned back in April last year, research has shown that getting 8 hours of sleep a night is important for optimal cognitive function. We all know how crappy we feel when we’re sleep-deprived. Brain fuzz takes over. We start to yawn uncontrollably in an effort to oxygenate our exhausted neurons. Our eyes start hurting and feeling dry, prompting us to rub them for relief. Every horizontal surface starts to look attractive. But there is a lot more to it than just feeling lousy.

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Weather bugs

Posted on March 11, 2012 by gydle

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?

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The measure of things

Posted on February 29, 2012 by gydle

The headline caught my eye back in September, and I knew it was a subject that I had to write about for Gydle. I stashed it in my “writing ideas” bookmark folder and there it sat, waiting. Last week, an article appeared in the local paper, reminding me. And then yesterday it hit – today, February 29, is the perfect day to write about this.

Did you know that the kilogram is losing weight? So you, therefore, are gaining weight?

But, you say, a kilogram isn’t a thing, it’s a measurement unit! You’re right, it’s one of the SI units, which together make up the solid mathematical foundation upon which all science is done. When you study science, you study units. Rule #1: make sure the units balance out.

(Well, if you’re an American, it’s more like First, stop thinking in feet and ounces. Then make sure the units balance out.)

A kilogram can’t lose weight! That’s just absurd.

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Colorful language

Posted on February 21, 2012 by gydle

I’m sure at some point in your life – even if only as a teenager under the influence – you’ve asked yourself this deep, philosophical question:

How do I know that what I’m experiencing is real?

The answer? You can’t. What you see as reality is unique to you, because it’s a complex interaction between the physical world, your senses and your brain.

As proof, here’s a little snippet from my reality:

It’s Tuesday. We’re on the top part of this week’s circle, heading counterclockwise in the direction of Wednesday. We’ve come out of Monday’s black zone successfully, and because Tuesday is red, I’m pretty energized. It’s February, which is my favorite color (green), so all is well. We’re heading clockwise towards March, which is mauve and located at roughy 8 o’clock on the circle of 2012. I think a bit more about the word I described in my last post, plebiscite, and realize that because of the p and b, it’s a very blue word. Could that have been why I didn’t associate it with approval, which is much more yellow-orange, despite the double p?

What? Continue reading →

Make me care

Posted on January 24, 2012 by gydle

I mentioned last week that I had somehow gotten through the filters and was accepted as part of the audience for last Friday’s TEDx Lausanne conference. I was really excited, because I am a huge TED fan. I’ve listened to lots of TED talks on the internet, and been very inspired. TED’s motto “Ideas worth sharing,” resonates with me. I’m an idea person.

So there I was, nametag around my neck: Self-Employed. I should have put CEO, Gydle Publishing Empire but I didn’t realize I’d get it on a nametag. Oh well, next time. Other people’s nametags also sported words describing things they cared about: virtual reality, world peace, vegetarianism, Internet of Things. I think it was supposed to be a conversation-starter. Since I’d apparently left this bit blank on the registration form, I just roamed around, not conversing. That was okay, because Nespresso co-sponsored the event and so there was plenty of coffee.

Maybe I set myself up for disappointment. Maybe listening to the best TED talks on the internet didn’t prepare me for this reality: very few people know how to give a good talk. Out of a hundred 15-minute talks, you’re lucky to get about ten good ones. On Friday we were lucky, because a few were relatively decent. But nothing really inspired me. The organizers of the conference probably will blacklist me for this, but when it was over, oddly enough I felt kind of like the girl in the conference’s homepage image (above): disconnected. What was that we just sped past?

During the breaks, I had some interesting conversations with people who weren’t intimidated by my lack of professional affiliation; and after the talks were over I met some of the speakers and talked with them as well. They’re great people who are quite passionate about their work. It must be scary as hell to give a TEDx talk to an audience secretly hoping to hear somebody like Al Gore or Sir Ken Robinson. (I hope none of them read my blog. If you’re reading this, you know who you are, I think you’re great and keep up the good work…).

I’m not going to deconstruct the talks here, or my conversations with other attendees, even though there were some interesting ideas exchanged in both venues. Instead I’m going to share what I thought about during most of the conference, at least when I wasn’t thinking about what I should have put on my nametag or why none of the speakers was talking about gamification, given that the theme of the conference was ostensibly the future. Which was: What makes for a good TED talk?

At about 3:30 pm, I had an epiphany of sorts: In fact, a good TED talk isn’t about the speaker at all. It’s not about the audience, either. It transcends all those individual egos. A good TED talk is really just a novel form of energy transfer.

In a good talk, the passionate idea in the speaker’s head somehow takes hold of the heads and hearts of the audience. In a good talk, the speaker builds a connection with the audience using words, pictures, laughter and silence, until a kind of mental bridge forms between them and energy flows freely through the room. The audience ends up really, truly caring. If you hooked them up to brain wave monitors, I’m guessing their hippocampi would be lighted up like Christmas trees. The idea is shared. It’s emotional, it’s inspiring and above all, it’s uplifting.

In a good talk, the audience doesn’t have to work to follow the talk or to be inspired. No, quite the contrary: it’s practically impossible for them not to be inspired, not to care, to remain indifferent. Unless, of course, they’re psychopaths. But the likelihood of an audience of psychopaths at a TEDx conference is pretty slim – even in California. Certainly not in Lausanne.

So next time you have to give a talk, I challenge you to think about this energy transfer: Why do you care about your idea? Where is its energy coming from? Dig deep and find the source of your passion, the place where it all starts. Tap into that. That’s the story the audience wants to hear. Look into their eyes, work some magic with words, pictures, jokes and pregnant pauses, and then beam it out there, Scotty.

Disclaimer: I am not a public speaking expert. I would probably give a horrible talk, although I’d try hard not to. For some really useful tips on how to give a speech, I do actually know a real public speaking expert, John Zimmer, and he has a blog called Manner of Speaking. I recommend it.

Photo Credit: Ward. via Compfight cc

Storytelling

Posted on January 18, 2012 by gydle

Last fall, I promised to do a series of posts on cognitive biases. A cognitive bias, in case you’re not familiar with the term, is a kind of built-in mental shortcut that we take when making decisions. Usually, we’re not aware we’re doing it.

Here’s a classic example, the framing bias: You’re sitting in front of a bunch of potential investors. What do you tell them – A: that your product has a 1 in 10 chance of succeeding, or B: that it has a 90% chance of failure? Doh.

Here’s another, the anchoring bias. You’re in a store. Everything on the rack is over $200. You see a sweater for $50. What a good deal! Now you’re in another store. Everything on the rack is under $50. You see the exact same sweater, for $50. Not such a good deal after all?

I’ve been doing a bit of reading on the subject, and it turns out we’re brimming with biases. We think we’re rational, that we can look objectively at a situation or listen to someone and weigh his or her words impartially, but we can’t. We’re highly illogical creatures bound up in a complex net of emotion and suggestion, living under the illusion that our brains work like computers.

It’s so bad that I’ve totally lost my desire to write about it. If you’d like to get depressed, too, here’s a short reading list:

Part of my disgust stems from my observation that the current political charade that is going on in the US, otherwise known as the Republican Primaries, is a stunning and vivid example of how to exploit most of these biases. Biases like the exposure effect, in which you tend to increasingly prefer something when you are repeatedly exposed to it (like a face or a slogan), and the illusion-of-truth effect, in which you are more likely to believe a statement is true if you have heard it before – whether or not it really is true. That the machine so blatantly exploits our cognitive weaknesses should perhaps not come as a surprise, but I still find it deeply disappointing and disturbing.

Perhaps the most interesting thing I’ve taken away from all this reading is that humans have an innate need to tell a story. We may vary somewhat in our tendency to make irrational decisions, to act on instincts that lie far beneath the surface of our consciousness, but the one thing we all have in common is our need to create a narrative that ties it all together. We do something or make a choice, and then we make up a story to explain why we did the thing or made the choice. Experiment after experiment has shown this to be the case. That’s what most of the billions of neurons inside those big brains of ours are doing: making up stories to rationalize our knee-jerk reactions.

We’re storytelling machines.

I think it’s high time we stopped settling for fairy tales, where everything is nice and simple – good versus evil, rags-to-riches, a stranger came to town – and started insisting on stories that reflect the real complexity of the world we live in. Then I think we might actually have a fighting chance of making decisions that would benefit us and our children in the long run.

Here’s a snippet from a TED talk on the subject by Tyler Cowen. I highly recommend you watch the talk or read the transcript. And then think about the political landscape. Then pass the Prozac.

One interesting thing about cognitive biases – they’re the subject of so many books these days. There’s the Nudge book, the Sway book, the Blink book, like the one-title book, all about the ways in which we screw up. And there are so many ways, but what I find interesting is that none of these books identify what, to me, is the single, central, most important way we screw up, and that is, we tell ourselves too many stories, or we are too easily seduced by stories.

So what are the problems of relying too heavily on stories? You view your life like “this” instead of the mess that it is or it ought to be. But more specifically, I think of a few major problems when we think too much in terms of narrative. First, narratives tend to be too simple. The point of a narrative is to strip it way, not just into 18 minutes, but most narratives you could present in a sentence or two. So when you strip away detail, you tend to tell stories in terms of good vs. evil, whether it’s a story about your own life or a story about politics. Now, some things actually are good vs. evil. We all know this, right? But I think, as a general rule, we’re too inclined to tell the good vs. evil story. As a simple rule of thumb, just imagine every time you’re telling a good vs. evil story, you’re basically lowering your IQ by ten points or more. If you just adopt that as a kind of inner mental habit, it’s, in my view, one way to get a lot smarter pretty quickly. You don’t have to read any books. Just imagine yourself pressing a button every time you tell the good vs. evil story, and by pressing that button you’re lowering your IQ by ten points or more.[…]

If the presidential candidates followed this rule, lowering their IQ by 10 points every time they told a good versus evil story, they’d be brain dead by now. Wait. They are! Welcome to the world of zombie politics.

I saw a video the other day on YouTube, classic Newt Gingrich blasting Mick Romney. You know what he saves for last? The ultimate thing that should slam Romney into the ground, make him a laughing stock, un-electable? Hint: he shares it with John Kerry.

You’ll have to see it to believe it.

Now, enough depressing stuff. Here’s the good news: Somehow I got through the quality control filter and snagged a spot in Friday’s TEDx Lausanne audience! I’m particularly looking forward to a talk by Steve Edge, who describes himself as “Designer, branding guru, dyslexic and madman.” More on that next week.

Image: wingedwolf

Epiphanies

Posted on January 6, 2012 by gydle

It’s January 6th, epiphany. This is the day the three kings apparently saw baby Jesus for the first time. Epiphany comes from the Greek word epiphaneia, “appearance” or “manifestation.” The Greeks were referring to things like the appearance of the sun on the horizon at dawn, an enemy, or a god.

When the word “epiphany” is used in English today, it usually refers to an idea or an unusually profound insight. I’ve had an epiphany! Marc exclaims. Maybe my stomach hurt because I had two apples, five kiwis and four cups of coffee before heading out for my run today! (actually, in all fairness, he probably wouldn’t have said epiphany. He’d probably just say I just thought of something. And I’d reply, Did it hurt? And then he’d tell me about his gastric situation and I’d say, well, doh, what did you expect?)

That an epiphany can be both the physical manifestation of something or someone as well as a purely cerebral manifestation of insight – a light bulb going off in your head – is an oddly apt illustration for our times, in which the boundaries between the virtual and the physical worlds seem to be increasingly hard to pin down.

Oh, I see. What an epiphany.

One current buzz phrase is “augmented reality” – if you’re interested, my friend the Spime Wrangler writes about the topic beautifully on her blog. It means that we infuse extra layers of meaning onto objects in the physical world. But what, really, is reality? We already experience the physical world through the filter of our oh-so-fallible senses. Add some Bailey’s, and my reality is definitely augmented, and in a good way. Come to think of it, does it make any sense at all to even talk about “reality” as such?

Over the holidays, on that long trans-Atlantic flight, I finally got a chance to read Incognito by David Eagleman, the one I told you was on the top of my list back in June when I wrote a post about inspiration. Here’s the thing. Reality, augmented or just garden-variety, is a construct. Seeing has very little to do with our eyes and everything to do with our brains, which are masters of taking what they can get and creating out of it a world in which we can survive. Eagleman uses the example of a man who has been blind most of his life. He has an operation that restores his vision. But his brain doesn’t know how to interpret the incoming data. None of it makes any sense to him. He can see, but he can’t “see.”

He gazed with utter puzzlement at the objects in front of him. His brain didn’t know what to make of the barrage of inputs. He wasn’t experiencing his sons’ faces; he was experiencing only un-interpretable sensations of edges and colors and lights. Although his eyes were functioning, he didn’t have vision. […] The strange electrical storms inside the pitch-black skull get turned into conscious summaries after a long haul of figuring out how objects in the world match up across the senses. Consider the experience of walking down a hallway. Mike knew from a lifetime of moving down corridors that walls remain parallel, at arm’s length, the whole way down. So when his vision was restored, the concept of converging perspective lines was beyond his capacity to understand. It made no sense to his brain.

Talk about feeling sea-sick! The amazing thing about this is that it took Mike’s brain only a few weeks to adapt. Now he sees just like you and I do.

Eagleman uses another example, this time a blind rock climber named Eric Weihenmayer, who in 2001 became the first blind person to climb Mount Everest. He “sees” using a grid of electrodes in his mouth, a device called a BrainPort.

Although the tongue is normally a taste organ, its moisture and chemical environment make it an excellent brain-machine interface when a tingling electrode grid is laid on its surface. The grid translates a video input into patters of electrical pulses, allowing the tongue to discern qualities usually ascribed to vision, such as distance, shape, direction of movement and size. The apparatus reminds us that we see not with our eyes but rather with our brains.

This kind of rocked my boat, particularly when Eagleman went on to reveal that the BrainPort is also being used to feed infrared or sonar input to the tongue so that divers can see in murky water of soldiers can have 360-degree vision. Eyes in the back of your head, indeed. Just one page later, I had to put the book down so my brain wouldn’t overheat. Here’s why:

In the future we may be able to plug new sorts of data streams directly into the brain, such as infrared or ultraviolet vision, or even weather data or stock market data. The brain will struggle to absorb the data at first, but eventually it will learn to speak the language. We’ll be able to add new functionality and roll out Brain 2.0. […] this is not a theoretical notion; it already exists in various guises.

Now why anyone would want stock market data plugged directly into their brains is beyond me, but I know Marc would love a direct feed from ESPN.

That’s probably enough to chew on for one day. This wide, wonderful world is already amazing, even with the limited sensory apparatus we’re born with. Just thinking about what more might be out there – the rich smell and sound experience of the dog, the razor-sharp vision of the eagle, the reverberating echoes of the bat – well, it’s tempting, isn’t it? But remember that just because a data stream can be piped in, that doesn’t mean our brains will know what to do with it. That five-pound lump between our shoulders is notoriously fallible when it comes to decision-making and rationalizing.

So here’s the epiphany of the day: Be like the Greeks. Watch a sunset. Watch your enemy approach over a far-off hill. See the face of the gods in the clouds outside an airplane window. And when the light bulb of ephiphany goes off in your brain, remember that your brain is a fallible organ, eager to create meaning from nothingness, and bask in the wonder of it all.

Lightbulb image: Shuttermonkey

Out with a bang

Posted on December 31, 2011 by gydle

Happy New Year, everyone. Looks like the world made it through another revolution around the Sun, despite Harold Camping’s careful calculations.

I have it on good faith, however, that it really is going to end in 2012. Yes, it’s more eschatological stuff, this time from the “Mesoamerican Long Count Calendar” (e.g. the Mayans). So set your clocks for December 21, 2012, and get all your unfinished business out of the way by then. I know I’m going to finish this novel and to hell with everything else. Taxes, schmaxes. What a colossal waste of time.

One thing I might do to get ready is memorize the Scrabble dictionary. If I end up in heaven with a lot of time on my hands, I don’t want to be at a disadvantage like I was this Christmas. On the other hand, that would be a pretty convincing version of hell — being in an endless Scrabble game with three other people who know every single esoteric word in the Scrabble dictionary. Of course ‘ka’ is a word! Isn’t it just too bad that it blocked you from putting ‘quiz’ on the triple word score…

I think I’ll play it safe and do the memorizing.

Looking back at 2011, I’d have to say it was a watershed year. Here are some highlights:

I started the Gydle publishing empire. I have written more original words this year than ever before in my life.
My world was rocked when I figured out that we are being crowdsourced by bacteria. I certainly hope yours was, too.
My bare feet discovered that the ground is a surface that can bite back.
I finally gave myself permission to live my lifelong dream – (the novel).
I learned that I’m not 25 anymore thanks to a surprise sucker punch from a blood pressure monitor.
I finally broke my jelly belly addiction. I may have to change the banner on the blog. Sugar snap peas? Carrots?

What about you? What did you do in those precious months after May 21, when the world was supposed to end? I certainly hope you made the most of it.

In the meantime, since I’m clearly too late for any preventive measures, before you go to bed tonight, take a vitamin B supplement and an advil. It might help with tomorrow’s hangover, according to a press release from the Loyola University Medical System.

And if the world is spinning because you drank too much? Here’s why.

On a final note in this final hour of the penultimate year of human existence, I’d like to thank all of you for coming here. Thanks for your attention and support. Thanks for your comments, your suggestions, your ideas. Thanks for making all my efforts so very worthwhile. Thanks for joining me in my many-flavored world and for making it so much more interesting!

See you in 2012!
Photo Credit: sunsurfr via Compfight cc

Fold It!

Posted on December 13, 2011 by gydle

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.

Yawn

Posted on November 16, 2011 by gydle

Monday afternoon, I couldn’t stop yawning. Sure, I was tired – I’ve been writing thousands of words a day on top of endless little bits and pieces of translating that keep dribbling in – but this was unusual. Later that afternoon, I saw this:

Yawning may no longer be a wide open question

Worth a click. I wasn’t aware that yawning was one of the great unsolved problems of science.

A dentist from the University of Maryland School of Dentistry (Gary Hack) and a Princeton postdoc (Andrew Gallup) claim that we don’t yawn because we’re tired, sleepy, or need more oxygen.

No, they say, we yawn in order to cool down our brains. Continue reading →