BRAIN Initiative: Thoughts on Interim Report to the NIH

neurons reconstructed in eyewire, connectome

We stand on the verge of a great journey into the unknown—the interior terrain of thinking, feeling, perceiving, learning, deciding, and acting to achieve our goals—that lives within the human brain. These capacities are the essence of our minds and the aspects of being human that matter most to us. Remarkably, these powerful yet exquisitely nuanced capacities emerge from electrical and chemical interactions among roughly 100 billion nerve cells and glial cells that compose our brains. All human brains share basic anatomical circuits and synaptic interactions, but the precise pattern of connections and interactions are highly variable from person to person—and therein lies the source of the remarkable variation we see in human behavior, from the breathtaking dance of a ballerina, to the elegant craftsmanship of a master carpenter, to the shrewd judgment of an expert trader. Our brains make us who we are, enabling us to perceive beauty, teach our children, remember loved ones, react against injustice, learn from history, and imagine a different future.

Preamble, The Goals of the BRAIN Initiative

Today is my one year anniversary at MIT. I’ve grown as a person and learned more than I ever imagined. To celebrate, I read a 50+ page NIH report, which was surprisingly awe inspiring. Here are my thoughts.

On Sept 16, 2013, an advisory committee of prominent neuroscientists presented a report to the NIH Director outlining the goals and objectives of the BRAIN Initiative for FY 2014.

Before we proceed, Iet’s back up. My greatest passion in life is understanding consciousness; understanding how the brain yields a thinking, feeling human being. That’s why I’m at Seung Lab working on EyeWire, attempting to catalyze exponential progress advancing neuroscience from the unknown into the understood. How exciting, how chill-inducing to read that the greatest minds on minds of our generation are teaming up and calling for unprecedented action in this direction, progress backed with investment and goals for disruptive, interdisciplinary collaboration that “reconceives what it means to be an experimental neuroscientist.” (13)

The report outlines several themes and high-priority research areas for 2014:

  1. Generate a Census of Cell Types
  2. Create Structural Maps of the Brain
  3. Develop New Large-Scale Network Recording Capabilities
  4. Develop A Suite of Tools for Circuit Manipulation
  5. Link Neuronal Activity to Behavior
  6. Integrate Theory, Modeling, Statistics, and Computation with Experimentation
  7. Delineate Mechanisms Underlying Human Imaging Technologies
  8. Create Mechanisms to Enable Collection of Human Data
  9. Disseminate Knowledge and Training

I am particularly excited about, well, all of these but for the interest of time I’ll hone it down. First, let’s reflect on the fact that we don’t even know how many types of cells there are in our own heads..and how quickly that’s changing. A catalog of cell types would provide a framework for existing research and a foundation for future experiments. Like everything in this report, it’s extremely exciting.

Second. Create a structural map of the brain. The report calls for a movement “towards [mapping] a full connectome.” Oh yes. There are many layers of functional circuits in the brain, all of which are important to our broader understanding. Special emphasis is given to integrating scales in both time and space and creating platforms that “enable understanding of the relation between neural structure and function.” The report calls for “faster, less expensive, and scalable approaches” that will reveal how how neural dynamics relate to complex behavior. Crowd-sourcing is specifically mentioned in this section, which needless to say amps me up.

neuron branches, eyewire,

I’ll skip now to numbers 5 and 6, which read as a call for revolutionary cross-boundary collaboration among researchers to create integrative tools for creating enriched, multidimensional datasets that, for example, might integrate molecular, functional and connectomic information. The report indicates a preferences for involvement from fields outside neuroscience such as computer science, statistics, engineering, physics and theory (and even calls for new theoretical tools and techniques — a “brain based theory of higher functions is notably lacking.” hello, opportunity).

This is not the time to play is safe.

I love this. Neuroscience is due a bit of disruption; we need to bring in minds from different fields — fields that the authors of this report may not have even considered, such as design. I think crucial components will be identifying and communicating neuroscience’s biggest accomplishments, current state of knowledge and present/future hurdles to communities of talented individuals and organizations, many of which may be outside academia, who will develop and test innovative solutions to them. We may use tools like Kaggle or host Hackathons, challenging a burgeoning global developer community to create software that will help solve neuroscience’s biggest difficulties. I’ve come to realize that while techniques do cost a considerable amount of time, it seems that software and big data analysis are what’s really needed to increase technolgical and analytical throughput by 100-1000x, as the report calls for. One infamous case of analytic delay is that of Earl Miller’s Lab at MIT. The team spent 2 weeks collecting functional activity data and 2 years analyzing it. Damn. We need tools, better AI and brave collaborations on all neruoscientific fronts. This is one area I’m particularly interested in catalyzing.

Another interesting component of this research is an open call to create a neuroscience data reservoir where researchers can store and one day maybe even crowd-source analysis of their research findings, specifically image data. Seung Lab (my lab) has an interest in this, so stay tuned.

synapse in eyewire

A final point of interest is #9, the dissemination of knowledge and training. In the context of citizen science, which will likely play an increasingly important role in neuroscientific progress, we need to share best practices and methods through which labs can involve the general public in the scientific method. We are actively working on such toolkits and events. Ping me if you are interested in collaborating on this or any other area.

Finally, going back to the big picture (my favorite), I’d like to point out that the report specifically calls for research “composed with a specific eye toward eventual impact for humans” and that “encourages changes in the culture of neuroscience.”

The challenge is to map the circuits of the brain, measure the fluctuating patterns of electrical and chemical activity flowing within those circuits, and understand how their interplay creates our unique cognitive and behavioral capabilities.

Our ultimate goal is to understand our own brains.. to understand the circuits and patterns of neural activity that give rise to mental experience and behavior.

It’s a wonderful time to be alive. I’m honored to have the opportunity to play a leading role in the future of neuroscience through EyeWire and specifically Seung Lab at MIT.

for science eyewire black on yellow, for science, eyewire, brain, design

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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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Idea flow

Sitting outside. A storm approaches.  Strong air. Thinking about life, ideas, posture, air quality, metabolic networks, connectomics, neuroscience, biomimicry, dynamic architectures, infographics many things.  How do I choose what to blog about?  Which idea arrays generate the most spikes of late.. how am I most passionate?  What ideas are most valuable to you, for you to think, to stimulate your own mind?  Hm exploring other minds, understanding and fueling curiosity, exploring what exists.. What ideas spark me as splendid and why.  That’s what I will blog about.

Neuroscientists are combining viral addictive game mechanics with EM resolution imaging analytics of 3D brain tissue. Game changer.

Background: you are the connections among your neurons.  Humans have never mapped this “connectome.”  Not even of a mouse.  Some scientists did c. elegans, a 1 mm worm with 4,000 total connections.  It took 12 years.  You have 100 billion neurons, some with tens of thousands of connections.

Researchers use a blend of AI and manual mapping to trace the 3D shape of neurons (colorful picture above).  It takes 1,000 lab hours to map 1 cubic milimeter of tissue.  How big is a full brain?  One million times larger.  We’re working to solve the bottleneck by crowd-sourcing the analytics. Sebastian Seung’s lab at MIT conceptualized a game called WiredDifferently (because we are, and we must map it to see and understand ourselves) and built a live beta that allows users to help map retinal connectivity at the synaptic level by filling in a 3D coloring book of sorts (we don’t even know how we see!).  I will write more about this on

Is this splended? You decide.  I experience joy by thinking about neural network complexity and the sheer magnitude of challenge. We don’t even know how many different types of cells there are in our own heads!  Opportunity.  Time to accelerate the rate of exponential progress.  Develop new questions, technologies, understandings..

Other splendidities..

Language.  How does the way I think reflect a configuration of neurons?  I wonder.

Quora continues to fuel surprise discoveries.  Exploring how others explore fascinates me.  I love navigating thoughts with questions.  There is an entire network of ideas growng now.  Splended! You can be a part of it.  See how my ideas evolve. And check out these stats about your body.  Visualize..

What might you find curious…Last week was in San Fran working on the MIT project, before that was in Dubai and Doha for TEDxSummit (blog that) and prior to that TEDMED.  Hyper development in the past couple months.  Exceptional connectivity in rare environments catalyzes rapid idea prototyping.  Theories are evolving. More on that before the end of the year. For now, launched Healthy City pilot with DailyFeats; the TEDx Global Music Project was granted forward progress by TED, other projects hm this post is about what, making you think? You want to hear thoughts that come out of experiences.  Alright.

The Exploratorium: epic interactive museum.  These are whoa.

Uncoupled “simple” pendulum waveforms.

Magnetic sand (black and magnetic because it contains iron)

Ferrofluids, strongly magnetizable fluids.

In conclusion, think something new, think differently frequently.  Here’s a drop of surprise that I happened upon on Quora to get you on your way: what is the most badass ancient city?

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Google Body: the awesome report

Google Body is gone, ladies and gentlemen.  It was lost in a changeover from google labs.  “More wood behind fewer arrows,” says Google.  For now, what was google body is not available for use.  I hope the next version includes deep tissue zoom.

Google “google body” and you find Zygote Labs, the imaging and design firm that created the brain and heart below.

by Zygote 3D anatomy

Zygote is the company behind the 3D human anatomy displayed in Google Body.  As Google Labs winds down Zygote will move forward with Zygote Body.

A “searchable and interactive 3D model of human anatomy.”  Awesome.

I hope that interactive body3D incorporates agility.  I imagine that one could input a movement relative to neutral position and the digital anatomy moves as it were a human body and you can zoom into deep muscle layers etc and see which ones are flexing and how much etc.  zoom from whole body to biomolecular happenings.  I’m thinking.  It’s on now.

Imagination squared.

Notes on a blog:

This is individual reporting.  I think someday I will run these blog posts through a grammatical analytics platform and map the trajectories of my concentrated and directional ideas.  This post is a catalog, occuring over more minutes than you might think.

I’m looking around the Zygote/3Dscience website.  They have a curious program called Human Factors, which

“enables users to use anthropometrically accurate solid 3D male and female models within their SolidWork assemblies to visualize and evaluate …[one hopes musculoskeletal] interaction [of the human body] with the human body [are these hard to read?  I just wrote two varities of the incident sentence. As a reader of these thoughts some time in the future, I wonder what relevance the previous grammatical bifurcation might encourage.]”

$950 licensing fee.  Google body, you were free!  I think humanity is trending toward freedom of innovation.  I think it compounds when shared.  And the best part, action from ideas!

Welcome to my mind.  9:40 on a Tuesday evening. In between writing on this post I did 2 handstands.  Relevant?  Notes for future reference.  I am creating a book.

What else do I do.  What is a blog?

I ask questions.  They give life moguls and amplitude, and curious word combinations.  What does that mean, thinking differently?  Relative to myself, how do my neural networks change relative to how they used to be and where and how and with whom could I explore this?

I learned recently two cognitive curiosities:

  1. Every neuron in your brain has its own capillary.
  2. Dendritic spining is an integral part of your neurons’ function and evolution.
“The modification of synaptic connections between neurons is thought to underlie our ability to form memories and acquire new behaviors. The majority of excitatory synapses in the brain are formed onto specialized cellular structures known as dendritic spines that consist of a bulbous spine head that is separated from the remainder of the dendrite by a thin neck.”

Says Neurobiology Professor Bernardo Sabatini of Harvard Medical School’s Department of Neurobiology.  Dendritic spines seem to serve the purpose of spatially segmenting individual synapses such that signal transductions are not interfered with by neighboring synapses.  The volume of a spine is tiny at <1 femtoliter (one quadrillionth of a liter).  We have only recently been able to image them and observe their interaction in living tissue.  Here is the latest comprehension of how they work:

“spines are dynamic structures that grow, structurally reorganize, and sometimes disappear within tens of minutes and spine motility has been correlated with the ability of animals of reorganize their cerebral cortex..”

This spawns a plethora of thoughts in various directions which I will think more thoroughly through then communicate the most valuable aka curious ones to you, the internet and me, myself.  For now, on with the train of thought.

A blog is self notes.  I think of it as making my mind social.

How do I share how I think?  Is that what I actually think about?  When?  With most passion?  Curiosity?  Time?  How does what I do/what I spend time thinking about (and doing) vary over time?  It is in bursts.  What do I think about in my spare time?  Why do I suddenly experience shyness?

Finishing up, the awesome report: things interesting to me.  Think and discover and enjoy!

“Non-profit global collaborative experiment to collect health and lifestyle information and share it in an open and anonymous way.”

google chrome experimental

Google Experimental. I am testing Google Instant.

“Google is always experimenting with new features aimed at improving the search experience. Take one for a spin.”

Quora:  The Wikipedia of Questions

“A continually improving collection of questions and answers created, edited, and organized by everyone who uses it.”

New arXiv entries into the journal of Quantitative Biology.

Look at these categories!

  • molecular networks
  • neurons and cognition
  • subcellular processes
  • biomolecules
  • cell behavior

11:56 pm.  Final words, thoughts?  Exist mindfully and intensely.

Life is long if you know how to use it.

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