What does the world look like through the eyes of a neuroscientist?

connectome project

How does the world look through the eyes of neuroscience?

Paul King of the Redwood Center for Theoretical Neuroscience at UC Berkeley sums up his perspective in 7 points on Quora:

1. Body image is dynamic and flexible.
2. Perceptual reality is entirely generated by our brain.
3. We see the world in narrow disjoint fragments.
4. Our behavior is mostly automatic.
5. Our brain can fool itself in really strange ways.
6. Neurons are really slow.
7. Consciousness can be subdivided.

Read the full answer on the EyeWire Blog.

Image courtesy of the Laboratory of NeuroImaging at UCLA and Martinos Center for Biomedical Imaging at MGH, Consortium of the Human Connectome Project.

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Be More Epic

be more epicFriends, we live in a fucking amazing world. Turn on the news and you might never realize it; however, there is a cure for the pessimism. It’s called content curation. Much in the same way that BrainPickings curates the web’s interestingness and I Fucking Love Science + It’s Okay To Be Smart make science awesome and accessible to everyone, I’ve launched a new experiment in collaborative epicness called Be More Epic.

This new Facebook Page is curated by a small group of people whose minds I love. The guidelines are simple: share whatever strikes you as epic.

On this page you will find an integration of epicness from the world’s best and most obscure sources. We primarily share from RedBull, National Geographic, GoPro and other rad media powerhouses. You’ll also find crazy pics and videos of shit you never knew existed, such as thisthis and this.

Like the page and share what strikes you as epic on our wall. If you’re interested in contributing to curation, message me.

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It’s human nature to want to explore

I have mad respect for RedBull, an energy drink company turned powerhouse of epic. RedBull supports adventure. They embrace risk. They empower people to break bones and boundaries. Here’s their latest video, which is awesome.

I hear you like the wild ones, honey, is that true? Yes, yes it is.  I curate amazing, wild things from Red Bull on a new Facebook page called Be More Epic.

Transcript:

“I think it’s human nature to want to explore.

Find your line and go beyond it.

The only limit is the one you set yourself.”

Images brought to you by RedBull:

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What if Google ads were replaced with inspirational words? It’s happening to me.

Holstee Manifesto, inspireWhat if when you visited an ad-supported website, you were shown the Holstee Manifesto?

Back in December I saw an ad for Holstee. For the first time ever, I clicked (and ended up buying inspiring notecards printed on 50% elephant poo). Since that fine day, Holstee has been stalking me.

And I love it.

I read about monkeys plaguing Puerto Rico and Holstee is there. I browse Colossal; Holstee is there. NYT, WSJ, YouTube..Holstee is there.  There’s really nothing like clicking on a link and getting a thumbnail of “share your passion” or even better — while wasting time on Reddit, “life is short” pops up and jolts my supernova self back into focus.

I occasionally click the ads and buy more things from Holstee, as much in joy to share their kind words with friends as to keep these awesome ads in my browser.

Have you ever experienced something like this? Have you ever tried hacking Google Ads?

In case you need visual proof, here are a couple screenshots:

monkeys plague puerto rico

Screen Shot 2013-01-02 at 1.09.26 AM Screen Shot 2013-01-07 at 8.42.52 PMScreen Shot 2013-01-04 at 11.37.34 AM

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Live Broadcast from the Shoulders of Giants or How (Funny) Videos Augment Science Communication

In the past week, over 10,000 people have joined EyeWire, a citizen science neuron mapping game from Seung Lab at MIT.

I’m about 8 weeks new in this wonderful lab and have started mixing things up a bit. What do typical researchers do on a daily basis? Who knows! They’re spectacular and secretive creatures. Seung Lab is not so secretive. Dev ninjas have even started doing spontaneous video sessions (who knew you could catch a ninja on video?!) and our whole team hosted a G+ hangout during a Christmas party, which might have included copious amounts of alcohol, dancing and wouldn’t have been complete without popping champagne. Our cameras are locked and loaded — charged and mic’d up. Don’t you love it when scientists have personality (yea that’s a GIF of Sebastian dancing created by EyeWirer Dylan Holtz), a sense of humor and are willing to share it with the world? I sure as hell do. I think it makes science more attractive and accessible, which is, in the words of brewery Sam Adams, always a good decision.

As you can see, we take science — but not ourselves —  seriously here.

i dont always pretend to be a scientist but when I do it's on EyeWire.org

That was created by EyeWirer Adam Brabant.

Seriously, though, Why EyeWire? You could read this post….or watch the video below.

We interviewed Harvard’s Joshua Sanes (a legend among neuroscientists.. though admittedly I did not know this chap until I learned he discovered a new cell, which made me wonder: if the EyeWire community discovers new cells, do they get to name them?  If I have anything to say about it, new cells will not be called “Junctional Adhesion Molecule B” Cells. No, no. I’d opt for the “epic” neuron so that people come to know us as the Discoverers of Epic).

A little EyeWire Tutorial:

A fun video we made when I Fucking Love Science + Reddit crashed EyeWire on Tuesday:

More videos are coming, including action-packed theatrical trailers, ultramicrotome drama, and dancing (lots of dancing) from Sebastian. Oh yea, and educational productions. After all, we do want to create a smarter world. I leave you with this: Sebastian goes Gangnam style. Created by Seung Lab’s great Spaniard postdoc Ignacio aka Nacho.

“Discover what is to be taken seriously and laugh at the rest,” Herman Hesse.

Want more examples of rad science videos making a splash? Check out

ASAP Science | Dr. Carin Bondar’s Wild Sex (Biology Series) | TED-Ed

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A bit of what I’ve been up to at MIT

I recently moved to Cambridge, MA to take the best job of all time helping Sebastian Seung’s Computational Neuroscience Lab at MIT build a game to map the human brain. Yea. It’s called EyeWire and you should check it out.

Best job in the world for several reasons. For someone obsessed with thinking about thinking, this life is positively dreamy.  I think I live one solid series of awesome moments. I love the people in my lab. I got to move to Cambridge and live one mile from Harvard and one mile from MIT. I love walking to work. I love work! It doesn’t feel like a job. I love going to hackathons. I love hanging out with geniuses. I love MIT Media Lab. I love working with neuroscientists. I love learning new things. I love being around curious people ready to share their passion for creating game-changing technologies. I love going to intellectual events at MIT and Harvard. I love connecting with so many TEDxers on the east coast! I love snow (though we haven’t had much yet). I love great food and even greater company. I love talking about molecules and python and infographics and chilling with scientists every day. Bascially, I love life. I love life very much.

I’m aslo helping a group at the Media Lab (which I’m not really supposed to talk about), developing a new app for TEDx music (also not supposed to talk about..but no one reads this blog 😉 and building an anonymized open-source database of health and lifestyle data with WIkiLife. Other things too..but it’s late and I want to read Nietzsche.

Below is a post I just wrote for the EyeWire blog. I blog at MIT now. Rad. Life is amazing. I hope you, dear reader, are following you passion and pursuing diligently the ideas that strike you most curious.  Reality will exceed your wildest expectations if you let it.

Cheers, much love.

Amy

It may come as a surprise that although we know much about how the eye works, neuroscience researchers do not fully understand how visual signals translate into perception.

We’ve landed on Mars, can grow organs, and even skydive from space, yet when it comes to a thorough understanding of the territory so close to home that it is home, much is missing. Neuroscientists don’t even know precisely how many different types of cells are in the brain. Here at Sebastian Seung‘s Computational Neuroscience Lab at MIT, we’re taking a different approach: crowd-sourcing. In order to solve the mind’s great mysteries, we need you.

Why don’t we know how the mind works? One reason is that your mind is massive. Researchers estimate that there are 100 billion neurons in your brain with about one million miles of connectivity. A million miles is equivalent to driving around Earth 40 times. You can infer that in order for such great length of neurons to fit into your three micron scale image by FSUpound brain these structures must be very tiny. A large neuron is about 100 microns in diameter while the contact area of a synapse is about 400 nm in length.

In order to see neurons and the tiny structures called dendrites through which they function, researchers utilize a new imaging technique. “Fix whole brain tissue, slice off layers just a few microns thick, image each slice with an electron microscope, and trace the path of each neuron,” explains David Zhou, Masters Student at Carnegie Mellon, on Quora. These gamechanging techniques generate terabytes of data for even a cubic milimeter of brain tissue. Now that we can see the brain at the synaptic scale, we have to analyze the images. How?

neuron cell reconstruction Seung Lab

The image above shows the process of layering image slices to render 3D reconstructions. Like most neuroscience labs, the Seung Lab uses a combination of AI algorithms and tracing (3D reconstruction) performed by humans. Why not just use algorithms? Images can be challenging to identify, particularly for a computer. Pure algorithms make many mistakes, such as slicing a single cell into thousands of pieces and merging multiple cells into one monstrously massive neuron. See below image for an example of AI missing a chunk of a neuron.

correcting a computer's mistake, Seung Lab

We hope to one day train computers to map neurons on their own; however, that day will be far in the future and we need to accelerate neuroscience discovery now. To achieve this, we need something more intelligent than even the most powerful supercomputer— you.

It takes an MIT-trained neuroscientist anywhere from 15 to 80 hours to reconstruct a single neuron. At that rate, it would take about 570,000,000 years to map the connectivity of an enture human brain, known as aconnectome. This is why we need your help.

Rather than mapping and entire brain, we’re starting with a retina. Our goal is to map the connections of a specific type of cell: J-Cells. These neurons are responsible for perception of upward motion. We plan to publish the outcome in a scientific journal and list EyeWire users as co-authors.

By playing the 3D game Eyewire, you become part of the Seung Lab at MIT by helping to map the connections of a neural network.

Scientific American writes that “no specialized knowledge of neuroscience is required [to play EyeWire]; citizen scientists need only be curious, intelligent and observant. Your input will help scientists understand how the retina functions. It will also be used by engineers to improve the underlying computational technology, eventually making it powerful enough to detect “miswirings” of the brain that are hypothesized to underlie disorders like autism and schizophrenia.”

We hope that you will help us trace the wires of perception through EyeWire. Play EyeWire and let us know what you think on Facebook.

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See the World Differently with Beautiful Photomicrography

Before you read this, pause and look at your hand.  Imagine that you could see ten, one hundred, a thousand times higher resolution.  What would your hand look like?  What world the world look like?

Photomicrography, the science of imaging through microscopes, is a window into an exotic world.

To illustrate the beautiful new perspectives made possible by advanced imaging technology, I’ve compiled some exquisite images from Nikon Small World.  Can you identify them? You’re doing well if you get even one correct. Answers are at the bottom of this post.

1.

cricket tongue

2.

tapeworm head

3.

compound shrimp eye

4.

red ink mixed with acid, heated

5.

feather of a dove

6.

"fruit fly eye"

7.

"marine diatom"

8.

"moth wing"

9.

"crystallized mix of resorcinal, methylene blue and sulphur"

10.

"fossilized shells"

11.

"soap bubbles"

12.

"wrinkled photoresist"

13.

"actin bundles" image

14.

"cup fern longitudinal section" image

15.

"water crystal" image

16.

"bird of paradise seed"

17.

"Butterfly egg on pink powderpuff bud"

18.

microchip

19.

sand magnified 4x

20.

"mushroom gills"

Answers:

1. Cricket tongue by Christian Gautier

2. Head of a tapeworm by Vigar Zaman

3. Shrimp eye by John Douglass

4. Red ink mixed with acid, heated by Carlos Jimenez Perez

5. Feather of a dove by Leonard Cannone

6. Fruit fly eye by Guichuan Huo

7. Marine diatom by Wim Van Egmond

8. Moth wing by Charles Krebs

9. Crystallized mix of resorcinal, methylene blue and sulphur by John Hart

10. Fossilized shells by Wim van Egmond

11. Soap bubbles by Viktor Syorka

12. Wrinkled photoresist by Pedro Barrios-Perez (what is a photoresist?)

13. Actin bundles by Dennis Breitsprecher

14. Cup fern, longitudinal rhizome section by Stephen Lowry

15. Water crystal by Raul Gonzalez

16. Bird of paradise (plant) seed by Viktor Syorka

17. Butterfly egg on pink powderpuff bud by David Millard

18. Microchip by Alfred Paseika

19. Sand by Yanping Wang

20. Mushroom gills by Charles Krebs

A few more awesome images that may surprise you:

Pollen grains by Shirley Owens

Lysine by Nikolai Vsevolodov

Small intestine of mouse by Paul Appleton

All images sourced from Nikon’s Small World.

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A Bucket List

US Presidential Elections 2012 have me thinking about awesomeness.   Ironically, the time of year that America divides decisively into two halves, seemingly uniting only in declaring their unfettered hate of each another, makes me think about how much I love it when these sentiments don’t dominate conversation. Remember that time when we landed Curiosity on Mars?  Remember how awesome that was?  Yes, you do.  Humanity rocks.

Tonight seems appropriate, then, to dig up and publish the old Bucket List.  That’s right – I have one. It’s in Google Docs. I keep it real(time updated).

The magna carta of Amyian wonderfuel:

 

Amy’s Bucket List

 

  • Go to space
  • Wild Life:
    • swim with pink river dolphins in Amazon (more info. note: attract these curious creatures with music and splashing)
    • climb the inside of a strangler fig (more info)
    • new: see (annndmaybe play with) fairy penguins in Australia (tiniest penguins on earth at 14”, bay near Pearson islands northern coast)
    • run through fields of: blooming lavender, dutch tulips, a blooming south african meadow
    • play with tiny monkeys (Miami, FL..wherever)
    • Apoka via Karl
    • hike to the boiling lake on Dominica via Karl
  • Speak at TED (done-ish..but do more solidly 🙂
  • Own a ridiculously fast, energy efficient convertible (all our patents are belong to you)
  • live in Asia
  • learn Mandarin
  • become good at Javascript
  • skydive in a wingsuit somewhere with beautiful scenery
  • have sex in space
  • be able to balance a handstand for one minute (as of June 2014: 10 seconds haha. Sept 2016: ~10 seconds)
  • EXPLORE/Adventure
    • see Indonesian blue lava by helicopter or something
    • Ko Tapu (James Bond Island)
    • Torres del Paine (Chile)
    • Great Blue Hole, Belize
    • Baiyang Waterfall Trail in Taiwan info
    • New Years on Copacabana Beach in Rio de Janeiro, Brasil
    • Machu Picchu
    • Mendenhall Glacier, alaska (vid)
    • Slickrock Trail, Moab
    • night dive in waters inhabited by bioluminescent creatures (more info)
    • visit a living bridge in rural indian jungles (more info)
    • The Beach of the Cathedrals, Ribadeo, Spain
    • The Moeraki Boulders (Dragon Eggs) In Koekohe Beach, New Zealand
    • Giants Causeway Beach, Ireland
    • Panjin China – red beach (go in Autumn)
    • Arrecife Alacran http://www.gulfbase.org/reef/view.php?rid=arrecife14
  • become proficient in advanced maths
  • jump off the roof of a building into:
    • a pile of snow
    • a swimming pool
  • ride a giraffe
  • become a National Geographic Explorer
  • Beethoven’s 9th challenge
  • figure out consciousness
  • Visit every country on Earth.
  • visualize global air quality data
  • film some time Lapses (macro and hyper)
    • more to come… (as of June 2014)

Bucketed!

    • skydive (done!)

    • run through a field of flowers (done!)

    • learn to surf (done!)

    • play with penguins (done! in Dubai)

    • speak at the white house (April 2014, EyeWire)

    • Run through field of sunflowers (2016)

 

  • So far I’ve been to:

    1. Aruba

    2. Bahamas

    3. Belgium

    4. Canada

    5. Costa Rica

    6. Dubai/UAE

    7. England

    8. Egypt

    9. France

    10. Germany

    11. Greece

    12. Mexico

    13. Netherlands

    14. Nicaragua

    15. Panama

    16. Qatar

    17. Spain

    18. Switzerland

    19. Turkey

    20. UAE

    21. ..USA + PR

 

No time like the present, as Tibolt says, to “take action on your ideas.  Action generates inspiration!”

First, four Bucket List Accomplishments:

1. Learn to Surf

Completed: August 2009

One summer I happened upon a housesitting gig in Honolulu, Hawaii.  Thanks to a nicely timed Facebook status update from an old high school friend (these were the days when we weren’t constantly fbing) and a spontaneous me, I decided that if I did not take this opportunity to live in Hawaii, I would probably regret it in five years. On two weeks notice, I hauled out. A month later I checked surfing off the bucket list.

A sensible bucket lister would include things like summiting a volcano or cliff jumping..but no, the only thing that counted towards bucket lis mastery on that excursion was in fact learning to surf.  Shaka and mahalo to my lovely local friends who patiently waited as I battled swell after swell before finally hanging ten. Below: Brent Nakano, little sister Sara who came out to visit, and yours truly.

2. Run through a field of flowers

Completed: April 2011

It was so great that I didn’t just run through them, I sprawled out and basked in the awesomeness of 360 degree pink-tipped clover. And then I added more flower sprints to my Bucket List futures.

3. Skydive

Completed: Summer 2004

The summer after high school, I decided to jump out of a plane. This is the decision process that goes into most of my bucket list feat completions, or life in general.  I want to X. I do X. There is a video of this dive..somewhere.  The guys who made it liked heavy metal and as I recall it’s set to limp bizkit. Rock on, 2009 bro.

4. Play with penguins

Completed: April 2012

Because who doesn’t want to hug a penguin? They’re fucking awesome. Tiny feathered tuxedoed demolishers of fish with winds apparently strong enough to break an adult’s femur yet the little buggers still can’t get airborne. This shenanigan actually got me published in the Huffington Post via Quora (a most amazing social network).

That’s it.  In 26 long years I’ve completed four Bucket List items. A whopping one item every 6.5 years. Better step it up if I want to finish in my one and only lifetime.

Next, Future adventures:

  • Go to space
  • Have sex in space
  • new: run through fields of: blooming lavender, dutch tulips and a blooming south african meadow
  • Visit Machu Picchu
  • Speak at TED
  • Own a ridiculously fast, energy efficient convertible sports car
  • live in Asia
  • new: skydive in a wingsuit somewhere with beautiful scenery
  • be able to balance a handstand for one minute
  • New Years on Copacabana Beach in Rio de Janeiro, Brasil
  • become proficient in the most advanced mathematics
  • jump off the roof of a building into: a pile of snow; a swimming pool
  • ride a giraffe
  • scuba dive in waters inhabited by bioluminescent creatures

That’s my entire bucket list. I also want to understand consciousness but that doesn’t really feel appropriate next to “live in Asia,” it’s not really a bucket list item so much as the purpose of my life.

Now, thanks in part to US elections, my bucket list is public. You should make yours public, too. Inspire people!  Make a google doc of your bucket list and publish it on the web. Share a link in the comments or post it on Quora.

Finally, the point of this post is to overcome partisanship and remember human awesomeness. I’ll leave you with a #lifebonus video from my friend John Boswell, the beautiful mind behind Symphony of Science:

 

 

 


 

Want to tackle one? Talk up!

I blogged about this once.

Consider answering “What is on your bucket list?” on Quora.

don't take life too seriously

*remember not to take life too seriously*

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