Gamers Solve Problem that Dogged Researchers for Decades

“Online gamers have achieved a feat beyond the realm of ‘Second Life’ or ‘Dungeons and Dragons’: they have deciphered the structure of an enzyme of an AIDS-like virus that had thwarted scientists for a decade.”

Awesome. The takeaway I see in this approach is evocative of self-experimentation. Gamers are basically lots of little experimenters. Perhaps gamers succeeding where scientists had failed for a decade is less about playing a (purposeful) game for fun and more about simply having enough people iterating on the problem with a basic incentive to succeed (it’s fun).

Read more: http://www.smh.com.au/digital-life/games/online-gamers-crack-aids-enzyme-puzzle-20110919-1kgq2.html#ixzz1YPrBQ3yL

Online gamers crack AIDS enzyme puzzle

(snippet)

Figuring out the structure of proteins is vital for understanding the causes of many diseases and developing drugs to block them.
But a microscope gives only a flat image of what to the outsider looks like a plate of one-dimensional scrunched-up spaghetti. Pharmacologists, though, need a 3D picture that “unfolds” the molecule and rotates it in order to reveal potential targets for drugs.
This is where Foldit comes in.
Developed in 2008 by the University of Washington, it is a fun-for-purpose video game in which gamers, divided into competing groups, compete to unfold chains of amino acids – the building blocks of proteins – using a set of online tools.
To the astonishment of the scientists, the gamers produced an accurate model of the enzyme in just three weeks.
Cracking the enzyme “provides new insights for the design of antiretroviral drugs”, says the study, referring to the medication to keep people with the human immunodeficiency virus (HIV) alive.
It is believed to be the first time that gamers have resolved a long-standing scientific problem.
“We wanted to see if human intuition could succeed where automated methods had failed,” Firas Khatib of the university’s biochemistry lab said in a press release.
“The ingenuity of game players is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems.”
One of Foldit’s creators, Seth Cooper, explained why gamers had succeeded where computers had failed.
“People have spatial reasoning skills, something computers are not yet good at,” he said.
“Games provide a framework for bringing together the strengths of computers and humans. The results in this week’s paper show that gaming, science and computation can be combined to make advances that were not possible before.”

Failure to Move is the State of Paralysis

I keep returning to the idea of action (doing) over inaction (thinking). I also have been likening doing vs. thinking as similar to producing vs. consuming.   The problem with the consumption/production dichotomy is that the lines aren’t always clear as to which is which.  Sometimes you have to consume to produce.

Things I consume:

  • food/energy/time (necessary consumption)
  • blogs/books/tweets/email (some necessary, some unnecessary)
  • television (almost entirely unnecessary)

Things I produce:

  • blog posts/emails/ideas (derivative of consumption)
  • work/research/analysis (requires consumption)
  • art
  • well-being

What I mean by producing “well being” is that I create satisfaction through expending effort.  It seems that production takes effort.  I have to push my body through the mild discomforts of squatting 275 lbs. to have the satisfaction (as strange as it is) of a fatigued body.  I have to work through the mental gymnastics of writing out my thoughts to create a blog post.  I have to gather data and cajole understanding to create analysis.  It takes work.

Production has costs.

But perhaps the greatest cost of production is breaking the inertia of not doing anything at all.  Or worse still, imagining all the things you could (should) be doing but never doing any of them.  Not only does all of this low-grade effort fail to produce anything at all, it also reinforces thinking over doing.  It habitualizes inaction.  It amplifies the inertia.

This is why failure to move is the state of paralysis.  It’s a tautology, but it also boils down inaction to it’s most basic component: not doing.

I’ve  been thinking about this lately because I have so many ideas bubbling around in my head, most of which could be “big.”  And it’s that notion that these ideas have huge potential that makes me fear screwing them up.  Meanwhile, by nature of being “big,” they also have explicit costs.  I can very easily envision how much work they will take to make them succeed.  And wouldn’t you know it?  The more I think about them, the harder it becomes to act on them.

And like all productive efforts, all I have to do to break the state of paralysis is to move.

It is that simple.

How We Get Good at Something

It takes mundane, often boring, always repetitive practice. And often a whole lot of it. We learn by doing and not by thinking.

Watch this short creative take about Ira Glass’s advice on storytelling:

This strikes me as relevant to mastering any skill, and reminds me of George Leonard’s “Mastery” (a bit of a summary of Mastery can be found by Todd Becker, who prompted me to read Mastery in the first place — it’s a quick, inspiring/challenging book).

Watching that video reminds me of how I “became an artist.” I did a lot of art/cartooning as a kid and people would say to me, “You’re talented.” Being an artist was then, and still is today, looked at as some sort of “gift” bestowed from the heavens (and or my genetics). I’ve never believed this personally though.

How I became an artist was much simpler: I kept trying to copy the cartoon image of Super Mario over and over and over again, doing it better and better each time. I remember doing it 20-30 times one night for my classmates in maybe 1st grade. What I didn’t realize at the time was that I was inadvertently practicing how to copy something I saw with my eyes and put it down onto paper. Without any prompting or structured learning from parents or teachers, I trained myself as a five or six year old to draw cartoons.

This is the lunchbox that made me an artist:

A vintage plastic Aladdin Super Mario Bros. Lunch box - this is exactly what I used for lunch in early elementary school.
A vintage plastic Aladdin Super Mario Bros. Lunch box - this is exactly what I used for lunch in early elementary school.

This is how we learn: practice, perseverance, stumbling, and trial and error.

Back at it.

After an insanely long blogging hiatus, I’ve finally initiated a sitewide “upgrade:” I’m giving up on my old blogging platform (b2evolution, sorry buddy, we had some good times …) and have officially switched over to WordPress.  I’ve also picked up a shiny new WordPress theme via fellow Atlantan and friend John Saddington of TentBlogger.

I’m working on migrating all the old b2evo posts over to WordPress (hoping to enlist some help via a b2evo guru), so bear with me as I undergo this process.

In the meantime, here are a few things that I’m playing with:

  • BirthdayShoes.com — my overtly, bizarrely barefoot shoe fan site continues to grow as the minimalist footwear, barefoot running, and toe shoe movements ripple outward.  If I could just find the time to keep up with all the reviews I need to do!
  • Google — This is my dayjob here in the ATL.  Lately, I’ve been either researching the retail industry or playing with Google+ (Feel free to add me though if I don’t add you back, it’s probably because I’m having a hard time realizing who you are, so be sure to get my attention somehow).
  • Parenting — Do I really need to elaborate on this one?  Our youngest daughter is almost 2 and quite a handful.  Tack on the fact we recently moved into a house we bought in May and Sonal is pregnant (16 weeks today!) and life is busy.  Here’s Avi a few days ago telling me what to do!  The nerve . . . Stay right here, Daddy!
  • OEM Human (.com) This site is still extremely “beta.”  Hmm … maybe more “alpha.”  Anyway, this is a project I’ve had simmering on the backburner of my mind for at least a year now.  If you’re curious about it, be sure to sign up for the email subscription.
  • LeanGains — Been doing LeanGains for almost a year now.  Hope to post about the program soon.  Geez can’t believe it’s been almost a year.
  • Been quite interested in the impact of flavors on body set(ling)point per the works for Seth Roberts, Stephan Guyenet, and Todd Becker.
  • Recent reads include Beyond Brawn, The Brain that Changes Itself (awesome book), and most recently, Moonwalking with Einstein.
Hope to start posting more often here.  The blog needed a good reboot.  Here’s hoping this sticks.

Meatza! Meatza!

So last night I made a meatza for the second time. For those of you who’ve not had or heard of a meatza, it’s basically a pizza you make using ground beef for the crust.

I consider myself pretty carnivorous and I love pizza (Pizza and beer are make for the one-two punch to knock me completely off the paleo bandwagon*), but I have to confess: the notion of a meatza just didn’t appeal to me at first blush. Plus, I’d made a few attempts at the almond flour crust pizza and been a bit disappointed. It’s a lot of work to make an almond flour pizza, so when the result consistently disappointed, I just gave up on a low-carb pizza solution.

It was only when a few friends mentioned they had enjoyed meatza that I decided to give it a shot. I knew Richard had made meatza based off a meatza recipe from the Healthy Cooking Coach, so that’s where I scrounged up the basic directions.

Now, making a pizza is as simple as making a crust, adding toppings, and baking it in the oven. With a meatza then, the most complicated part here is making the crust. And it’s also the part that you’ve got to get right to make sure your meat pizza is delicious!

Enter my Italian grandfather’s meatball recipe. My Pop has a fairly famous (within the family anyway) spaghetti recipe for sauce and meatballs. I’m going to skip the sauce part for now because it’s a bit more labor-intensive. In a pinch, you can just use some spaghetti sauce from the store.

Anyway, it’s the meatball recipe that really knocks the meatza crust out of the park, so without further ado, here are the ingredients:

  1. I use a 12×17 rectangular pan
  2. Get a decent sized mixing bowl to mix the meat
  3. Start pre-heating the oven to 450
  4. For ease of mixing into the beef, I go ahead and get all my seasonings out and into a little bowl (this will make more sense in a second):
    • 1/2 cup grated Parmesan cheese**
    • 3 tsp salt
    • 1 tsp caraway seeds (this is the magic ingredient in my opinion)
    • 1 tsp oregano
    • 1 tsp garlic salt
    • 1 tsp coarse ground pepper
    • 1 tsp red pepper flakes (optional)
    • 2 lbs. ground beef (80/20 is fine)
  5. Seasonings mixed, put the beef into the mixing bowl, crack into it two eggs and mix beef and eggs first. This is because the runny egg can cause the seasonings to clump together and it just makes mixing a lot messier and less uniform if you don’t mix beef and egg first prior to adding the seasonings. Thus, the need for to pre-mix the seasonings — your hands are all covered in beef at this point, so you just have to pour in the seasonings!
  6. Add seasonings and Parmesan cheese and mix well! (Note: you can also do the Parmesan after the egg/beef pre-seasonings if you want)
  7. Take the mass of mixed beef and slam it onto your pan. BAM!
  8. Flatten it out: you should be able to just about cover a 12×17 pan with the beef
  9. Oven pre-heated, throw it in there for 10 minutes!

At this point, I immediately start pre-cooking certain ingredients that need a little extra attention; in my case, it’s sliced mushrooms and diced green pepper sauteeing in a cast iron skillet with some pasture butter.

Ten minutes up, take the crust out of the oven. Set the oven to Broil (it will take a few minutes to heat to this point).

You’ll now notice the crust has shrunk considerably and there’s a good bit of rendered fat in the pan. Pour the fat out of the pan. Optional step: take a paper towel and wipe up any extraneous beef “stuff” that is exterior to the crust. This is simply because it’s not part of the crust and if you leave it, it could cake to the pan and make clean-up more of a hassle.

Now, you just add your toppings. For me, I added Newman’s Sockerooni spaghetti sauce as a base, then a layer of pepperoni, then a base layer of mozarella cheese. From there, I add sliced green olives, feta cheese, the mushrooms and green peppers, more pepperoni, and top it all off with more cheese.

Broiler heated up, I throw it all back in the oven until the cheese is done. It cooks very fast at this point! Like five minutes is almost too long in our case, so make sure you keep a close eye on your meatza!

Take it out, let it sit for a minute or two, and slice and serve. I find this slices into six solid size pieces — I can eat a half a pizza under the right conditions, but one slice of meatza and I am good to go.

Enjoy!

Oh one more thing: I really like this alternative pizza combination. It is downright delicious and I don’t get that “sigh this isn’t really pizza” sensation at all. I’m not sure it is pizza, really, but it is really good, so who cares!

* Beer, chips, and salsa at Mexican restaurants being right up there, too.

** Were you to make the meatballs, you’d actually use two slices of bread, wet, and torn into small pieces OR 1 cup of plain bread crumbs (you can sub almond flour if you like)

Doctors make bad business people

http://blog.theentreprene…e-1#comment-464

Posting here a comment I left over at the Entrepreneur School Blog, where Jim Beach talks about the lack of business sense in doctors. If it sounds rant-ish, I apologize.

There are good reasons doctors make for bad business people (and entrepreneurs). The healthcare system is set up where the customer is an insurance company (1) and (2) practicing medicine has turned into a matter of treating symptoms rather than proactive care. In other words, the doctors expect *you* to call them when you have a problem because on the front-end (the preventative end) they largely have nothing to offer.

Case in point: medical students only take maybe a semester’s worth of nutrition. Insane when you consider that diet (and lifestyle) choices are certainly the most likely causes of people’s health maladies — so really, when it comes to having the proper tools to help patients avoid getting ill in the first place, doctor’s aren’t equipped. They are proactively/preventatively neutered.

I won’t get into the insurance company angle, but that has an impact, too. The customer has been utterly divorced from the healthcare system when you’ve got so many layers between you and your care:

you -> employer’s HR department -> [the insurance company bureaucracy] -> [hospital bureaucracy that negotiates reimbursement amounts] -> doctors who code procedures and provide you care

Simply cutting out the employer side would immediately get the consumer more plugged in as you’d have 10s of thousands of more individuals interested in getting better rates/plans from insurers than the lackadaisical corporate HR departments. I digress.

And there’s a (3) here, too. That’s that the doctor’s go to school for longer than any other profession, which makes them prone to dogmatism/procedure instead of being creative or driven to trial/error and problem-solving.

All things considered, it’s a disaster of a system. It’s no surprise it’s only getting worse. The only surprise (to me) is that so few people are talking about these core, simple problems that are making for such a disastrous healthcare system.

Collapse and Renewal

http://www.peopleandplace…se_and_renewal#

Found a lot of interesting things to think about in this article. Seems to get at how dynamic/complex/living systems (ecosystems, economies) evolve rapidly and then stagnate, which leads to collapse, and reboots the system (my simplification).

What I Have Learned
Change that is important is not gradual but is sudden and transformative. There is a common base cycle of change in individuals, in ecosystems, in business, in society. Increasing rigidity halts a long, slow period of growth and increasing efficiency. That begins a period of creative destruction and a fast period where uncertainty is great, where novelty emerges, and where new foundations are formed for a new cycle to begin. That is where we are now heading internationally.

In the United States, it is a time when the power of the state has achieved rigidity unseen since the triumphs of the falling of the Berlin Wall. Politicians have reacted to extreme disturbances, like the appalling terrorist attacks of 9/11, with powerful military response, a blind view of history and cultures, and a greedy desire for narrow benefit. Global economic expansion and dependence on peaking oil supplies, particularly in the Middle East, lock geopolitics into a self-destructive state from which transformation is extraordinarily difficult.

That is the time when change is most uncertain. We are living in it now. In this year we have simultaneously faced the sudden appearance of now reinforcing flips – sudden increases in the price of oil, increases in the costs of food, a financial collapse and the start of a recession, the retreat of Arctic ice sheets with climate warming, and accelerating loss of biodiversity. That is a lot to swallow and it reflects a process of human development and expansion since WWII.

But it is also the time when the individual has the greatest influence: when experiments determine the future; when the Internet opens opportunities for collaboration within and across nations; and when low cost mistakes are glorious because they trigger learning.

And these are the lessons I have learned that help in that process of dealing with turbulence:

1) Separate individual thought and work is essential but now, when integrative studies are the only way to reveal understanding, work with others is equally so. An individual’s knowledge can be combined with that of others to make the whole greater. In doing that we each recognize that we do not know everything but we do know, and know well, something. We learn with grace and humor and patience to work with others from different disciplines and backgrounds.

2) Complexity is in the mind of the beholder, in the patterns that are generated by causes that are simpler. Not as simple as once thought, but explained by a kind of “Rule of Hand”, not by a “Rule of Thumb’. Quite simply, I found in case after case of ecosystem change that four to six sets of variables operating at a number of different scales, in a non-linear way, captured nature’s flipping behavior. It turns out that ecosystems are temporary assemblages, pausing for a few hundreds of centuries in a passing state of quasi-stability as part of evolutionary change. Think of that when we think of the reality of global climate change.

3) There are about three kinds of scientists – the consolidator, the technical expert, and the artist. Consolidators accumulate and solidify advances and are deeply skeptical of ill formed and initial, hesitant steps. That can have a great value at stages in a scientific cycle when rigorous efforts to establish the strength and value of an idea is central. Technical experts assess the methods of investigation. Both assume they search for the certainty of understanding.

In contrast, I love the initial hesitant steps of the “artist scientist” and like to see clusters of them. That is the kind of thing needed at the beginning of a cycle of scientific enquiry or even just before that. Such nascent, partially stumbling ideas, are the largely hidden source for the engine that eventually generates change in science. I love the nascent ideas, the sudden explosion of a new idea, the connections of the new idea with others. I love the development and testing of the idea till it gets to the point it is convincing, or is rejected. That needs persistence to the level of stubbornness and I eagerly invest in that persistence.

All types of scientists are necessary, but I would love it if we could encourage and include the innovative type of artist. At the least, enjoy rigor, but never inhibit the innovative artists.

4) I learned that the key to make effective designs was to identify large, unattainable goals that can be approached, but not achieved, ones that relate to fundamental values of free speech, freedom, equity, tolerance and education. And then to add a tough design for the first step, in a way that highlights or creates options to design, later, a second step – and then a third and so on. We found that the results were steps that rapidly covered more ground than could ever be designed at the start. At the heart, that is adaptive design, where the unknown is great, learning is continual and actions evolve.

5) I am prodigiously curious about nature, and that triggers initial ideas. I am also terribly persistent and stubborn about developing and testing an idea that grabs me; at those times I am totally and narrowly focused, driven by the potential. That is what eventually makes an idea useful. So I conclude that natures create the idea; stubbornness makes it useful! But I have had to learn how to see nature. It is curiosity, anecdotes, funny correlations, jokes and metaphors that start that. It is new emerging theory that completes it.

One has to learn to develop senses that help us listen to intriguing voices that are hidden amongst the noise. Owlish ways to hear the rustle of the mouse. Do that and the future will be fun and rewarding. We all might even help, at this time of great change and threat, to develop further a world of justice, understanding and equity.

The Game-Changer

It’s been quiet here on the site lately as the game has changed. I’m four weeks into fatherhood, and those four weeks feel more like ten.

I’ve been trying to come up with an easy way to explain to others what being a new parent is like. It’s an emotional roller coaster. Living with a nooborn is like setting a kitchen timer on a two to three hour schedule that never stops resetting. Change a diaper, feed, comfort, put baby to sleep, knock a few things out around the house, rinse, repeat. It does not stop.

And there are the fussy times when you lose confidence in your ability to parent — can I soothe this baby? Maybe mother can try. Maybe this will work. Maybe not. These times make me realize just how little I’ve appreciated my own parents (Thank you mom and dad!).

And then there are the moments where she grins from ear to ear or unequivocally meets your eyes with hers. The pride and joy that springs from these moments is profound.

Everyone tells you “your life [as you know it] is over.” They’re right. Becoming a parent is a game changer. There are new requirements, new rules, new milestones, new joys, new sorrows, and on and on. And you learn about it all as you go along via trial and error. Googling helps, too.

Being a parent is an incredible experience.

Aviana a.k.a. “Project Aminowings” a Success

My daughter Aviana entered the world Monday night. She was a smidge under eight pounds, and (no bias I promise) she is beautiful. She is also amazingly intelligent, wanting to stay up all night in an effort to elucidate the experience of dreaming in the womb. Unfortunately, this means that between the hours of midnight and five of six in the morning, she is doing anything but dreaming!

Needless to say, “Project Aminowings” was a huge success and I am one proud papa.

Joel Salatin’s “Everything I want to do is illegal”

http://www.mindfully.org/…legal1esp03.htm

Richard Nikoley pointed me to this excellent essay by Polyface Farm’s Joel Salatin. It is one of the best things I’ve read in quite some time — a complete indictment of government interference with just wanting to be free. Joel suggests that eventually the noose will tighten too much and a cycle will assert itself once more, throwing off these heinous chains to freedom, individuality, diversity and independence. I hope he is right.

Look, if I want to build a yurt of rabbit skins and go to the bathroom in a compost pile, why is it any of the government’s business? Bureaucrats bend over back-wards to accredit, tax credit, and offer money to people wanting to build pig city-factories or bigger airports. But let a guy go to his woods, cut down some trees, and build himself a home, and a plethora of regulatory tyrants descend on the project to complicate, obfuscate, irritate, frustrate, and virtually terminate. I think it’s time to eradicate some of these laws and the piranhas who administer them.