Tag Archives: Brain Activity Map

Brain-on-a-chip 2014 survey/overview

Michael Berger has written another of his Nanowerk Spotlight articles focussing on neuromorphic engineering and the concept of a brain-on-a-chip bringing it up-to-date April 2014 style.

It’s a topic he and I have been following (separately) for years. Berger’s April 4, 2014 Brain-on-a-chip Spotlight article provides a very welcome overview of the international neuromorphic engineering effort (Note: Links have been removed),

Constructing realistic simulations of the human brain is a key goal of the Human Brain Project, a massive European-led research project that commenced in 2013.

The Human Brain Project is a large-scale, scientific collaborative project, which aims to gather all existing knowledge about the human brain, build multi-scale models of the brain that integrate this knowledge and use these models to simulate the brain on supercomputers. The resulting “virtual brain” offers the prospect of a fundamentally new and improved understanding of the human brain, opening the way for better treatments for brain diseases and for novel, brain-like computing technologies.

Several years ago, another European project named FACETS (Fast Analog Computing with Emergent Transient States) completed an exhaustive study of neurons to find out exactly how they work, how they connect to each other and how the network can ‘learn’ to do new things. One of the outcomes of the project was PyNN, a simulator-independent language for building neuronal network models.

Scientists have great expectations that nanotechnologies will bring them closer to the goal of creating computer systems that can simulate and emulate the brain’s abilities for sensation, perception, action, interaction and cognition while rivaling its low power consumption and compact size – basically a brain-on-a-chip. Already, scientists are working hard on laying the foundations for what is called neuromorphic engineering – a new interdisciplinary discipline that includes nanotechnologies and whose goal is to design artificial neural systems with physical architectures similar to biological nervous systems.

Several research projects funded with millions of dollars are at work with the goal of developing brain-inspired computer architectures or virtual brains: DARPA’s SyNAPSE, the EU’s BrainScaleS (a successor to FACETS), or the Blue Brain project (one of the predecessors of the Human Brain Project) at Switzerland’s EPFL [École Polytechnique Fédérale de Lausanne].

Berger goes on to describe the raison d’être for neuromorphic engineering (attempts to mimic biological brains),

Programmable machines are limited not only by their computational capacity, but also by an architecture requiring (human-derived) algorithms to both describe and process information from their environment. In contrast, biological neural systems (e.g., brains) autonomously process information in complex environments by automatically learning relevant and probabilistically stable features and associations. Since real world systems are always many body problems with infinite combinatorial complexity, neuromorphic electronic machines would be preferable in a host of applications – but useful and practical implementations do not yet exist.

Researchers are mostly interested in emulating neural plasticity (aka synaptic plasticity), from Berger’s April 4, 2014 article,

Independent from military-inspired research like DARPA’s, nanotechnology researchers in France have developed a hybrid nanoparticle-organic transistor that can mimic the main functionalities of a synapse. This organic transistor, based on pentacene and gold nanoparticles and termed NOMFET (Nanoparticle Organic Memory Field-Effect Transistor), has opened the way to new generations of neuro-inspired computers, capable of responding in a manner similar to the nervous system  (read more: “Scientists use nanotechnology to try building computers modeled after the brain”).

One of the key components of any neuromorphic effort, and its starting point, is the design of artificial synapses. Synapses dominate the architecture of the brain and are responsible for massive parallelism, structural plasticity, and robustness of the brain. They are also crucial to biological computations that underlie perception and learning. Therefore, a compact nanoelectronic device emulating the functions and plasticity of biological synapses will be the most important building block of brain-inspired computational systems.

In 2011, a team at Stanford University demonstrates a new single element nanoscale device, based on the successfully commercialized phase change material technology, emulating the functionality and the plasticity of biological synapses. In their work, the Stanford team demonstrated a single element electronic synapse with the capability of both the modulation of the time constant and the realization of the different synaptic plasticity forms while consuming picojoule level energy for its operation (read more: “Brain-inspired computing with nanoelectronic programmable synapses”).

Berger does mention memristors but not in any great detail in this article,

Researchers have also suggested that memristor devices are capable of emulating the biological synapses with properly designed CMOS neuron components. A memristor is a two-terminal electronic device whose conductance can be precisely modulated by charge or flux through it. It has the special property that its resistance can be programmed (resistor) and subsequently remains stored (memory).

One research project already demonstrated that a memristor can connect conventional circuits and support a process that is the basis for memory and learning in biological systems (read more: “Nanotechnology’s road to artificial brains”).

You can find a number of memristor articles here including these: Memristors have always been with us from June 14, 2013; How to use a memristor to create an artificial brain from Feb. 26, 2013; Electrochemistry of memristors in a critique of the 2008 discovery from Sept. 6, 2012; and many more (type ‘memristor’ into the blog search box and you should receive many postings or alternatively, you can try ‘artificial brains’ if you want everything I have on artificial brains).

Getting back to Berger’s April 4, 2014 article, he mentions one more approach and this one stands out,

A completely different – and revolutionary – human brain model has been designed by researchers in Japan who introduced the concept of a new class of computer which does not use any circuit or logic gate. This artificial brain-building project differs from all others in the world. It does not use logic-gate based computing within the framework of Turing. The decision-making protocol is not a logical reduction of decision rather projection of frequency fractal operations in a real space, it is an engineering perspective of Gödel’s incompleteness theorem.

Berger wrote about this work in much more detail in a Feb. 10, 2014 Nanowerk Spotlight article titled: Brain jelly – design and construction of an organic, brain-like computer, (Note: Links have been removed),

In a previous Nanowerk Spotlight we reported on the concept of a full-fledged massively parallel organic computer at the nanoscale that uses extremely low power (“Will brain-like evolutionary circuit lead to intelligent computers?”). In this work, the researchers created a process of circuit evolution similar to the human brain in an organic molecular layer. This was the first time that such a brain-like ‘evolutionary’ circuit had been realized.

The research team, led by Dr. Anirban Bandyopadhyay, a senior researcher at the Advanced Nano Characterization Center at the National Institute of Materials Science (NIMS) in Tsukuba, Japan, has now finalized their human brain model and introduced the concept of a new class of computer which does not use any circuit or logic gate.

In a new open-access paper published online on January 27, 2014, in Information (“Design and Construction of a Brain-Like Computer: A New Class of Frequency-Fractal Computing Using Wireless Communication in a Supramolecular Organic, Inorganic System”), Bandyopadhyay and his team now describe the fundamental computing principle of a frequency fractal brain like computer.

“Our artificial brain-building project differs from all others in the world for several reasons,” Bandyopadhyay explains to Nanowerk. He lists the four major distinctions:
1) We do not use logic gate based computing within the framework of Turing, our decision-making protocol is not a logical reduction of decision rather projection of frequency fractal operations in a real space, it is an engineering perspective of Gödel’s incompleteness theorem.
2) We do not need to write any software, the argument and basic phase transition for decision-making, ‘if-then’ arguments and the transformation of one set of arguments into another self-assemble and expand spontaneously, the system holds an astronomically large number of ‘if’ arguments and its associative ‘then’ situations.
3) We use ‘spontaneous reply back’, via wireless communication using a unique resonance band coupling mode, not conventional antenna-receiver model, since fractal based non-radiative power management is used, the power expense is negligible.
4) We have carried out our own single DNA, single protein molecule and single brain microtubule neurophysiological study to develop our own Human brain model.

I encourage people to read Berger’s articles on this topic as they provide excellent information and links to much more. Curiously (mind you, it is easy to miss something), he does not mention James Gimzewski’s work at the University of California at Los Angeles (UCLA). Working with colleagues from the National Institute for Materials Science in Japan, Gimzewski published a paper about “two-, three-terminal WO3-x-based nanoionic devices capable of a broad range of neuromorphic and electrical functions”. You can find out more about the paper in my Dec. 24, 2012 posting titled: Synaptic electronics.

As for the ‘brain jelly’ paper, here’s a link to and a citation for it,

Design and Construction of a Brain-Like Computer: A New Class of Frequency-Fractal Computing Using Wireless Communication in a Supramolecular Organic, Inorganic System by Subrata Ghoshemail, Krishna Aswaniemail, Surabhi Singhemail, Satyajit Sahuemail, Daisuke Fujitaemail and Anirban Bandyopadhyay. Information 2014, 5(1), 28-100; doi:10.3390/info5010028

It’s an open access paper.

As for anyone who’s curious about why the US BRAIN initiative ((Brain Research through Advancing Innovative Neurotechnologies, also referred to as the Brain Activity Map Project) is not mentioned, I believe that’s because it’s focussed on biological brains exclusively at this point (you can check its Wikipedia entry to confirm).

Anirban Bandyopadhyay was last mentioned here in a January 16, 2014 posting titled: Controversial theory of consciousness confirmed (maybe) in  the context of a presentation in Amsterdam, Netherlands.

US National Nanotechnology Initiative’s 2015 budget request shows a decrease of $200M

A March 27, 2014 news item on Nanowerk highlights the US National Nanotechnology Initiative’s (NNI) document titled “NNI Supplement to the President’s 2015 Budget” (86 pp. PDF; Note: A link has been removed),

This document (pdf) is a supplement to the President’s 2015 Budget request submitted to Congress on March 4, 2014. It gives a description of the activities underway in 2013 and 2014 and planned for 2015 by the Federal Government agencies participating in the National Nanotechnology Initiative (NNI), primarily from a programmatic and budgetary perspective.

The March 25, 2014 NNI announcement provides more details about the current request and funding over the years since the NNI’s inception,

The President’s 2015 Budget provides over $1.5 billion for the National Nanotechnology Initiative (NNI), a continued investment in support of the President’s priorities and innovation strategy. Cumulatively totaling nearly $21 billion since the inception of the NNI in 2001 (including the 2015 request), this support reflects nanotechnology’s potential to significantly improve our fundamental understanding and control of matter at the nanoscale and to translate that knowledge into solutions for critical national issues. The NNI investments in 2013 and 2014 and those proposed for 2015 continue the emphasis on accelerating the transition from basic R&D to innovations that support national priorities, while maintaining a strong base of foundational research, to provide a pipeline for future nanotechnology-based innovations.

The President’s 2015 Budget supports nanoscale science, engineering, and technology R&D at 11 agencies. Another 9 agencies have nanotechnology-related mission interests or regulatory responsibilities. The NNI Supplement to the President’s 2015 Budget documents progress of these NNI participating agencies in addressing the goals and objectives of the NNI. (See the Acronyms page for agency abbreviations.)

Courtesy: NNI [downloaded from http://www.nano.gov/node/1128]

Courtesy: NNI [downloaded from http://www.nano.gov/node/1128]

One significant change for the 2015 Budget, which is reflected in the figures provided in this document for 2013 and 2014, is a revision in the Program Component Areas (PCAs), budget categories under which the NNI investments are reported. Note that this represents an update of how NNI investments by the Federal Government are tabulated, but not a change in the overall scope of the Initiative. As outlined in the 2014 NNI Strategic Plan, the new PCAs are more broadly strategic, fully inclusive, and consistent with Federal research categories, while correlating well with the NNI goals and high-level objectives. Of particular note is the creation of a separate PCA for the Nanotechnology Signature Initiatives (NSIs), reflecting the high priority placed on NSIs in the 2015 OMB/OSTP R&D Priorities Memo.

The 2014 budget for the NNI was $1.7B (as per the NNI Supplement to the President’s 2014 Budget),

The President’s 2014 Budget provides over $1.7 billion for the National Nanotechnology Initiative (NNI), a sustained investment in support of the President’s priorities and innovation strategy. Cumulatively totaling almost $20 billion since the inception of the NNI in 2001 (including the 2014 request), …

So this year’s request represents a decrease of $200M. Coincidentally, the US BRAIN (Brain Research through Advancing Innovative Neurotechnologies) initiative (originally named BAM for brain activity map) is going to have its budget doubled from $100M in 2014 to $200M in 2015 (as per David Bruggeman’s March 25, 2014 posting on his Pasco Phronesis blog),

The President’s Fiscal Year 2015 (which starts on October 1, but likely won’t get funded until next February) budget rollout includes doubling support for the BRAIN (Brain Research though Advancing Innovative Neurotechnologies) Initiative.  The $100 million multi-agency (National Institutes of Health, Defense Advanced Research Projects Agency and National Science Foundation) public-private effort will have some of its first funding awards later this year.

Interesting, non?

For anyone interested in more specifics about the 2015 NNI budget request but who doesn’t want to read the supplementary document, you can visit this page.

Two bits about the brain: fiction affects your brain and the US’s BRAIN Initiative is soliciting grant submissions

As a writer I love to believe my words have a lasting impact and while this research is focused on fiction, something I write more rarely than nonfiction, hope springs eternal that one day nonfiction too will be proved as having an impact (in a good way) on the brain. From a Jan. 3, 2014 news release on EurekAlert (or you can read the Dec. 17, 2013 Emory University news release by Carol Clark),

Many people can recall reading at least one cherished story that they say changed their life. Now researchers at Emory University have detected what may be biological traces related to this feeling: Actual changes in the brain that linger, at least for a few days, after reading a novel.

“Stories shape our lives and in some cases help define a person,” says neuroscientist Gregory Berns, lead author of the study and the director of Emory’s Center for Neuropolicy. “We want to understand how stories get into your brain, and what they do to it.”

His co-authors included Kristina Blaine and Brandon Pye from the Center for Neuropolicy, and Michael Prietula from Emory’s Goizueta Business School.

Neurobiological research using functional magnetic resonance imaging (fMRI) has begun to identify brain networks associated with reading stories. Most previous studies have focused on the cognitive processes involved in short stories, while subjects are actually reading them while they are in the fMRI scanner.

All of the study subjects read the same novel, “Pompeii,” a 2003 thriller by Robert Harris that is based on the real-life eruption of Mount Vesuvius in ancient Italy.

“The story follows a protagonist, who is outside the city of Pompeii and notices steam and strange things happening around the volcano,” Berns says. “He tries to get back to Pompeii in time to save the woman he loves. Meanwhile, the volcano continues to bubble and nobody in the city recognizes the signs.”

The researchers chose the book due to its page-turning plot. “It depicts true events in a fictional and dramatic way,” Berns says. “It was important to us that the book had a strong narrative line.”

For the first five days, the participants came in each morning for a base-line fMRI scan of their brains in a resting state. Then they were fed nine sections of the novel, about 30 pages each, over a nine-day period. They were asked to read the assigned section in the evening, and come in the following morning. After taking a quiz to ensure they had finished the assigned reading, the participants underwent an fMRI scan of their brain in a non-reading, resting state. After completing all nine sections of the novel, the participants returned for five more mornings to undergo additional scans in a resting state.

The results showed heightened connectivity in the left temporal cortex, an area of the brain associated with receptivity for language, on the mornings following the reading assignments. “Even though the participants were not actually reading the novel while they were in the scanner, they retained this heightened connectivity,” Berns says. “We call that a ‘shadow activity,’ almost like a muscle memory.”

Heightened connectivity was also seen in the central sulcus of the brain, the primary sensory motor region of the brain. Neurons of this region have been associated with making representations of sensation for the body, a phenomenon known as grounded cognition. Just thinking about running, for instance, can activate the neurons associated with the physical act of running.

“The neural changes that we found associated with physical sensation and movement systems suggest that reading a novel can transport you into the body of the protagonist,” Berns says. “We already knew that good stories can put you in someone else’s shoes in a figurative sense. Now we’re seeing that something may also be happening biologically.”

The neural changes were not just immediate reactions, Berns says, since they persisted the morning after the readings, and for the five days after the participants completed the novel.

“It remains an open question how long these neural changes might last,” Berns says. “But the fact that we’re detecting them over a few days for a randomly assigned novel suggests that your favorite novels could certainly have a bigger and longer-lasting effect on the biology of your brain.”

Here’s a link to and a citation for the paper,

Short- and Long-Term Effects of a Novel on Connectivity in the Brain by Gregory S. Berns, Kristina Blaine, Michael J. Prietula, and Brandon E. Pye. Brain Connectivity. 2013, 3(6): 590-600. doi:10.1089/brain.2013.0166.

This is an open access paper where you’ll notice the participants cover a narrow range of ages (from the Materials and Methods section of the paper,

A total of 21 participants were studied. Two were excluded from the fMRI analyses: one for insufficient attendance, and the other for image abnormalities. Before the experiment, participants were screened for the presence of medical and psychiatric diagnoses, and none were taking medications. There were 12 female and 9 male participants between the ages of 19 and 27 (mean 21.5). Emory University’s Institutional Review Board approved all procedures, and all participants gave written informed consent.

It’s always good to remember that university research often draws from student populations and the question one might want to ask is whether or not those results will remain the same, more or less, throughout someone’s life span.In any event, I find this research intriguing and hope they follow this up.

Currently known as the BRAIN (Brain Research through Advancing Innovative Neurotechnologies), I first wrote about the project under its old name BAM (Brain Activity Map) in two postings, first in a March 4, 2013 posting featuring brain-to-brain communication and other brain-related tidbits, then again, in an April 2, 2013 posting featuring an announcement about its federal funding. Today (Jan. 6, 2014), I stumbled across some BRAIN funding opportunities for researchers, from the BRAIN Initiative funding opportunities webpage,

NIH released six funding opportunity announcements in support of the President’s BRAIN Initiative. Collectively, these opportunities focus on building a new arsenal of tools and technologies for helping scientists unlock the mysteries of the brain. NIH [US National Institutes of Health] plans to invest $40 million in Fiscal Year 2014 through these opportunities, contingent upon the submission of a sufficient number of scientifically meritorious applications.

The opportunities currently available are as follows:

  • Transformative Approaches for Cell-Type Classification in the Brain (U01) (RFA-MH-14-215) – aims to pilot classification strategies to generate a systematic inventory/cell census of cell types in the brain, integrating molecular identity of cell types with connectivity, morphology, and location. These pilot projects and methodologies should be designed to demonstrate their utility and scalability to ultimately complete a comprehensive cell census of the human brain.
    Contact Email: BRAIN-info-NIMH@mail.nih.gov
    Application Receipt: March 13, 2014
  • Development and Validation of Novel Tools to Analyze Cell-Specific and Circuit-Specific Processes in the Brain (U01) (RFA-MH-14-216) – aims to develop and validate novel tools that possess a high degree of cell-type and/or circuit-level specificity to facilitate the detailed analysis of complex circuits and provide insights into cellular interactions that underlie brain function. A particular emphasis is the development of new genetic and non-genetic tools for delivering genes, proteins and chemicals to cells of interest; new approaches are also expected to target specific cell types and or circuits in the nervous system with greater precision and sensitivity than currently established methods.
    Contact Email: BRAIN-info-NIMH@mail.nih.gov
    Application Receipt: March 13, 2014
  • New Technologies and Novel Approaches for Large-Scale Recording and Modulation in the Nervous System (U01) (RFA-NS-14-007) – focuses on development and proof-of-concept testing of new technologies and novel approaches for large scale recording and manipulation of neural activity, with cellular resolution, at multiple spatial and/or temporal scales, in any region and throughout the entire depth of the brain. The proposed research may be high risk, but if successful could profoundly change the course of neuroscience research.
    Contact Email: NINDS-Brain-Initiative@nih.gov
    Application Receipt: March 24, 2014
  • Optimization of Transformative Technologies for Large Scale Recording and Modulation in the Nervous System (U01) (RFA-NS-14-008) – aims to optimize existing and emerging technologies and approaches that have the potential to address major challenges associated with recording and manipulating neural activity. This FOA is intended for the iterative refinement of emergent technologies and approaches that have already demonstrated their transformative potential through initial proof-of-concept testing, and are appropriate for accelerated engineering development with an end-goal of broad dissemination and incorporation into regular neuroscience research.
    Contact Email: NINDS-Brain-Initiative@nih.gov
    Application Receipt: March 24, 2014
  • Integrated Approaches to Understanding Circuit Function in the Nervous System (U01) (RFA-NS-14-009) – focuses onexploratory studies that use new and emerging methods for large scale recording and manipulation to elucidate the contributions of dynamic circuit activity to a specific behavioral or neural system. Applications should propose teams of investigators that seek to cross boundaries of interdisciplinary collaboration, for integrated development of experimental, analytic and theoretical capabilities in preparation for a future competition for large-scale awards.
    Contact Email: NINDS-Brain-Initiative@nih.gov
    Application Receipt: March 24, 2014
  • Planning for Next Generation Human Brain Imaging (R24) (RFA-MH-14-217) – aims to create teams of imaging scientist together with other experts from a range of disciplines such as engineering, material sciences, nanotechnology and computer science, to plan for a new generation of non-invasive imaging techniques that would be used to understand human brain function. Incremental improvements to existing technologies will not be funded under this announcement.
    Contact Email: sgrant@nida.nih.gov
    Application Receipt: March 13, 2014

For the interested, in the near future there will be some informational conference calls regarding these opportunities,

Informational Conference Calls for Prospective Applicants

NIH will be hosting a series of informational conference calls to address technical questions regarding applications to each of the RFAs released under the BRAIN Initiative.   Information on dates and contacts for each of the conference calls is as follows:

January 10, 2014, 2:00-3:00 PM EST
RFA-MH-14-215, Transformative Approaches for Cell-Type Classification in the Brain

For call-in information, contact Andrea Beckel-Mitchener at BRAIN-info-NIMH@mail.nih.gov.

January 13, 2014, 2:00-3:00 PM EST
RFA-MH-14-216, Development and Validation of Novel Tools to Analyze Cell-Specific and Circuit-Specific Processes in the Brain

For call-in information, contact Michelle Freund at BRAIN-info-NIMH@mail.nih.gov.

January 15, 2014, 1:00-2:00 PM EST
RFA-MH-14-217, Planning for Next Generation Human Brain Imaging

For call-in information, contact Greg Farber at BRAIN-info-NIMH@mail.nih.gov.

February 4, 2014, 1:00-2:30 PM EST
RFA-NS-14-007, New Technologies and Novel Approaches for Large-Scale Recording and Modulation in the Nervous System
RFA-NS-14-008, Optimization of Transformative Technologies for Large Scale Recording and Modulation in the Nervous System
RFA-NS-14-009, Integrated Approaches to Understanding Circuit Function in the Nervous System

For call-in information, contact Karen David at NINDS-Brain-Initiative@nih.gov.
In addition to accessing the information provided in the upcoming conference calls, applicants are strongly encouraged to consult with the Scientific/Research Contacts listed in each of the RFAs to discuss the alignment of their proposed work with the goals of the RFA to which they intend to apply.

Good luck!

It’s kind of fascinating to see this much emphasis on brains what with the BRAIN Initiative in the US and the Human Brain Project in Europe (my Jan. 28, 2013 posting announcing the European Union’s winning Future and Emerging Technologies (FET) research projects, The prizes (1B Euros to be paid out over 10 years to each winner) had been won by the Human Brain FET project and the Graphene FET project, respectively

Nanotechnology and the US mega science project: BAM (Brain Activity Map) and more

The Brain Activity Map (BAM) project received budgetary approval as of this morning, Apr. 2, 2013 (I first mentioned BAM in my Mar. 4, 2013 posting when approval seemed imminent). From the news item, Obama Announces Huge Brain-Mapping Project, written by Stephanie Pappas for Yahoo News (Note: Links have been removed),

 President Barack Obama announced a new research initiative this morning (April 2) to map the human brain, a project that will launch with $100 million in funding in 2014.

The Brain Activity Map (BAM) project, as it is called, has been in the planning stages for some time. In the June 2012 issue of the journal Neuron, six scientists outlined broad proposals for developing non-invasive sensors and methods to experiment on single cells in neural networks. This February, President Obama made a vague reference to the project in his State of the Union address, mentioning that it could “unlock the answers to Alzheimer’s.”

In March, the project’s visionaries outlined their final goals in the journal Science. They call for an extended effort, lasting several years, to develop tools for monitoring up to a million neurons at a time. The end goal is to understand how brain networks function.

“It could enable neuroscience to really get to the nitty-gritty of brain circuits, which is the piece that’s been missing from the puzzle,” Rafael Yuste, the co-director of the Kavli Institute for Brain Circuits at Columbia University, who is part of the group spearheading the project, told LiveScience in March. “The reason it’s been missing is because we haven’t had the techniques, the tools.” [Inside the Brain: A Journey Through Time]

Not all neuroscientists support the project, however, with some arguing that it lacks clear goals and may cannibalize funds for other brain research.

….

I believe the $100M mentioned for 2014 would one installment in a series totaling up to $1B or more. In any event, it seems like a timely moment to comment on the communications campaign that has been waged on behalf of the BAM. It reminds me a little of the campaign for graphene, which was waged in the build up to the decision as to which two projects (in a field of six semi-finalists, then narrowed to a field of four finalists) should receive a FET (European Union’s Future and Emerging Technology) 1 billion euro research prize each. It seemed to me even a year or so before the decision that graphene’s win was a foregone conclusion but the organizers left nothing to chance and were relentless in their pursuit of attention and media coverage in the buildup to the final decision.

The most recent salvo in the BAM campaign was an attempt to link it with nanotechnology. A shrewd move given that the US has spent well over $1B since the US National Nanotechnology Initiative (NNI) was first approved in 2000. Linking the two projects means the NNI can lend a little authority to the new project (subtext: we’ve supported a mega-project before and that was successful) while the new project BAM can imbue the ageing NNI with some excitement.

Here’s more about nanotechnology and BAM from a Mar. 27, 2013 Spotlight article by Michael Berger on Nanowerk,

A comprehensive understanding of the brain remains an elusive, distant frontier. To arrive at a general theory of brain function would be an historic event, comparable to inferring quantum theory from huge sets of complex spectra and inferring evolutionary theory from vast biological field work. You might have heard about the proposed Brain Activity Map – a project that, like the Human Genome Project, will tap the hive mind of experts to make headway in the understanding of the field. Engineers and nanotechnologists will be needed to help build ever smaller devices for measuring the activity of individual neurons and, later, to control how those neurons function. Computer scientists will be called upon to develop methods for storing and analyzing the vast quantities of imaging and physiological data, and for creating virtual models for studying brain function. Neuroscientists will provide critical biological expertise to guide the research and interpret the results.

Berger goes on to highlight some of the ways nanotechnology-enabled devices could contribute to the effort. He draws heavily on a study published Mar. 20, 2013 online in ACS (American Chemical Society)Nano. Shockingly, the article is open access. Given that this is the first time I’ve come across an open access article in any of the American Chemical Society’s journals, I suspect that there was payment of some kind involved to make this information freely available. (The practice of allowing researchers to pay more in order to guarantee open access to their research in journals that also have articles behind paywalls seems to be in the process of becoming more common.)

Here’s a citation and a link to the article about nanotechnology and BAM,

Nanotools for Neuroscience and Brain Activity Mapping by A. Paul Alivisatos, Anne M. Andrews, Edward S. Boyden, Miyoung Chun, George M. Church, Karl Deisseroth, John P. Donoghue, Scott E. Fraser, Jennifer Lippincott-Schwartz, Loren L. Looger, Sotiris Masmanidis, Paul L. McEuen, Arto V. Nurmikko, Hongkun Park, Darcy S. Peterka, Clay Reid, Michael L. Roukes, Axel Scherer, Mark Schnitzer, Terrence J. Sejnowski, Kenneth L. Shepard, Doris Tsao, Gina Turrigiano, Paul S. Weiss, Chris Xu, Rafael Yuste, and Xiaowei Zhuang. ACS Nano, 2013, 7 (3), pp 1850–1866 DOI: 10.1021/nn4012847 Publication Date (Web): March 20, 2013
Copyright © 2013 American Chemical Society

As these things go, it’s a readable article for people without a neuroscience education provided they don’t mind feeling a little confused from time to time. From Nanotools for Neuroscience and Brain Activity Mapping (Note: Footnotes and links removed),

The Brain Activity Mapping (BAM) Project (…) has three goals in terms of building tools for neuroscience capable of (…) measuring the activity of large sets of neurons in complex brain circuits, (…) computationally analyzing and modeling these brain circuits, and (…) testing these models by manipulating the activities of chosen sets of neurons in these brain circuits.

As described below, many different approaches can, and likely will, be taken to achieve these goals as neural circuits of increasing size and complexity are studied and probed.

The BAM project will focus both on dynamic voltage activity and on chemical neurotransmission. With an estimated 85 billion neurons, 100 trillion synapses, and 100 chemical neurotransmitters in the human brain,(…) this is a daunting task. Thus, the BAM project will start with model organisms, neural circuits (vide infra), and small subsets of specific neural circuits in humans.

Among the approaches that show promise for the required dynamic, parallel measurements are optical and electro-optical methods that can be used to sense neural cell activity such as Ca2+,(7) voltage,(…) and (already some) neurotransmitters;(…) electrophysiological approaches that sense voltages and some electrochemically active neurotransmitters;(…) next-generation photonics-based probes with multifunctional capabilities;(18) synthetic biology approaches for recording histories of function;(…) and nanoelectronic measurements of voltage and local brain chemistry.(…) We anticipate that tools developed will also be applied to glia and more broadly to nanoscale and microscale monitoring of metabolic processes.

Entirely new tools will ultimately be required both to study neurons and neural circuits with minimal perturbation and to study the human brain. These tools might include “smart”, active nanoscale devices embedded within the brain that report on neural circuit activity wirelessly and/or entirely new modalities of remote sensing of neural circuit dynamics from outside the body. Remarkable advances in nanoscience and nanotechnology thus have key roles to play in transduction, reporting, power, and communications.

One of the ultimate goals of the BAM project is that the knowledge acquired and tools developed will prove useful in the intervention and treatment of a wide variety of diseases of the brain, including depression, epilepsy, Parkinson’s, schizophrenia, and others. We note that tens of thousands of patients have already been treated with invasive (i.e., through the skull) treatments. [emphases mine] While we hope to reduce the need for such measures, greatly improved and more robust interfaces to the brain would impact effectiveness and longevity where such treatments remain necessary.

Perhaps not so coincidentally, there was this Mar. 29, 2013 news item on Nanowerk,

Some human cells forget to empty their trash bins, and when the garbage piles up, it can lead to Parkinson’s disease and other genetic and age-related disorders. Scientists don’t yet understand why this happens, and Rice University engineering researcher Laura Segatori is hoping to change that, thanks to a prestigious five-year CAREER Award from the National Science Foundation (NSF).

Segatori, Rice’s T.N. Law Assistant Professor of Chemical and Biomolecular Engineering and assistant professor of bioengineering and of biochemistry and cell biology, will use her CAREER grant to create a toolkit for probing the workings of the cellular processes that lead to accumulation of waste material and development of diseases, such as Parkinson’s and lysosomal storage disorders. Each tool in the kit will be a nanoparticle — a speck of matter about the size of a virus — with a specific shape, size and charge.  [emphases mine] By tailoring each of these properties, Segatori’s team will create a series of specialized probes that can undercover the workings of a cellular process called autophagy.

“Eventually, once we understand how to design a nanoparticle to activate autophagy, we will use it as a tool to learn more about the autophagic process itself because there are still many question marks in biology regarding how this pathway works,” Segatori said. “It’s not completely clear how it is regulated. It seems that excessive autophagy may activate cell death, but it’s not yet clear. In short, we are looking for more than therapeutic applications. We are also hoping to use these nanoparticles as tools to study the basic science of autophagy.”

There is no direct reference to BAM but there are some intriguing correspondences.

Finally, there is no mention of nanotechnology in this radio broadcast/podcast and transcript but it does provide more information about BAM (for many folks this was first time they’d heard about the project) and the hopes and concerns this project raises while linking it to the Human Genome Project. From the Mar. 31, 2013 posting of a transcript and radio (Kera News; a National Public Radio station) podcast titled, Somewhere Over the Rainbow: The Journey to Map the Human Brain,

During the State of the Union, President Obama said the nation is about to embark on an ambitious project: to examine the human brain and create a road map to the trillions of connections that make it work.

“Every dollar we invested to map the human genome returned $140 to our economy — every dollar,” the president said. “Today, our scientists are mapping the human brain to unlock the answers to Alzheimer’s.”

Details of the project have slowly been leaking out: $3 billion, 10 years of research and hundreds of scientists. The National Institutes of Health is calling it the Brain Activity Map.

Obama isn’t the first to tout the benefits of a huge government science project. But can these projects really deliver? And what is mapping the human brain really going to get us?

Whether one wants to call it a public relations campaign or a marketing campaign is irrelevant. Science does not take place in an environment where data and projects are considered dispassionately. Enormous amounts of money are spent to sway public opinion and policymakers’ decisions.

ETA Ap. 3, 2013: Here are more stories about BAM and the announcement:

BRAIN Initiative Launched to Unlock Mysteries of Human Mind

Obama’s BRAIN Only 1/13 The Size Of Europe’s

BRAIN Initiative Builds on Efforts of Leading Neuroscientists and Nanotechnologists

Brain-to-brain communication, organic computers, and BAM (brain activity map), the connectome

Miguel Nicolelis, a professor at Duke University, has been making international headlines lately with two brain projects. The first one about implanting a brain chip that allows rats to perceive infrared light was mentioned in my Feb. 15, 2013 posting. The latest project is a brain-to-brain (rats) communication project as per a Feb. 28, 2013 news release on *EurekAlert,

Researchers have electronically linked the brains of pairs of rats for the first time, enabling them to communicate directly to solve simple behavioral puzzles. A further test of this work successfully linked the brains of two animals thousands of miles apart—one in Durham, N.C., and one in Natal, Brazil.

The results of these projects suggest the future potential for linking multiple brains to form what the research team is calling an “organic computer,” which could allow sharing of motor and sensory information among groups of animals. The study was published Feb. 28, 2013, in the journal Scientific Reports.

“Our previous studies with brain-machine interfaces had convinced us that the rat brain was much more plastic than we had previously thought,” said Miguel Nicolelis, M.D., PhD, lead author of the publication and professor of neurobiology at Duke University School of Medicine. “In those experiments, the rat brain was able to adapt easily to accept input from devices outside the body and even learn how to process invisible infrared light generated by an artificial sensor. So, the question we asked was, ‘if the brain could assimilate signals from artificial sensors, could it also assimilate information input from sensors from a different body?'”

Ben Schiller in a Mar. 1, 2013 article for Fast Company describes both the latest experiment and the work leading up to it,

First, two rats were trained to press a lever when a light went on in their cage. Press the right lever, and they would get a reward–a sip of water. The animals were then split in two: one cage had a lever with a light, while another had a lever without a light. When the first rat pressed the lever, the researchers sent electrical activity from its brain to the second rat. It pressed the right lever 70% of the time (more than half).

In another experiment, the rats seemed to collaborate. When the second rat didn’t push the right lever, the first rat was denied a drink. That seemed to encourage the first to improve its signals, raising the second rat’s lever-pushing success rate.

Finally, to show that brain-communication would work at a distance, the researchers put one rat in an cage in North Carolina, and another in Natal, Brazil. Despite noise on the Internet connection, the brain-link worked just as well–the rate at which the second rat pushed the lever was similar to the experiment conducted solely in the U.S.

The Duke University Feb. 28, 2013 news release, the origin for the news release on EurekAlert, provides more specific details about the experiments and the rats’ training,

To test this hypothesis, the researchers first trained pairs of rats to solve a simple problem: to press the correct lever when an indicator light above the lever switched on, which rewarded the rats with a sip of water. They next connected the two animals’ brains via arrays of microelectrodes inserted into the area of the cortex that processes motor information.

One of the two rodents was designated as the “encoder” animal. This animal received a visual cue that showed it which lever to press in exchange for a water reward. Once this “encoder” rat pressed the right lever, a sample of its brain activity that coded its behavioral decision was translated into a pattern of electrical stimulation that was delivered directly into the brain of the second rat, known as the “decoder” animal.

The decoder rat had the same types of levers in its chamber, but it did not receive any visual cue indicating which lever it should press to obtain a reward. Therefore, to press the correct lever and receive the reward it craved, the decoder rat would have to rely on the cue transmitted from the encoder via the brain-to-brain interface.

The researchers then conducted trials to determine how well the decoder animal could decipher the brain input from the encoder rat to choose the correct lever. The decoder rat ultimately achieved a maximum success rate of about 70 percent, only slightly below the possible maximum success rate of 78 percent that the researchers had theorized was achievable based on success rates of sending signals directly to the decoder rat’s brain.

Importantly, the communication provided by this brain-to-brain interface was two-way. For instance, the encoder rat did not receive a full reward if the decoder rat made a wrong choice. The result of this peculiar contingency, said Nicolelis, led to the establishment of a “behavioral collaboration” between the pair of rats.

“We saw that when the decoder rat committed an error, the encoder basically changed both its brain function and behavior to make it easier for its partner to get it right,” Nicolelis said. “The encoder improved the signal-to-noise ratio of its brain activity that represented the decision, so the signal became cleaner and easier to detect. And it made a quicker, cleaner decision to choose the correct lever to press. Invariably, when the encoder made those adaptations, the decoder got the right decision more often, so they both got a better reward.”

In a second set of experiments, the researchers trained pairs of rats to distinguish between a narrow or wide opening using their whiskers. If the opening was narrow, they were taught to nose-poke a water port on the left side of the chamber to receive a reward; for a wide opening, they had to poke a port on the right side.

The researchers then divided the rats into encoders and decoders. The decoders were trained to associate stimulation pulses with the left reward poke as the correct choice, and an absence of pulses with the right reward poke as correct. During trials in which the encoder detected the opening width and transmitted the choice to the decoder, the decoder had a success rate of about 65 percent, significantly above chance.

To test the transmission limits of the brain-to-brain communication, the researchers placed an encoder rat in Brazil, at the Edmond and Lily Safra International Institute of Neuroscience of Natal (ELS-IINN), and transmitted its brain signals over the Internet to a decoder rat in Durham, N.C. They found that the two rats could still work together on the tactile discrimination task.

“So, even though the animals were on different continents, with the resulting noisy transmission and signal delays, they could still communicate,” said Miguel Pais-Vieira, PhD, a postdoctoral fellow and first author of the study. “This tells us that it could be possible to create a workable, network of animal brains distributed in many different locations.”

Will Oremus in his Feb. 28, 2013 article for Slate seems a little less buoyant about the implications of this work,

Nicolelis believes this opens the possibility of building an “organic computer” that links the brains of multiple animals into a single central nervous system, which he calls a “brain-net.” Are you a little creeped out yet? In a statement, Nicolelis adds:

We cannot even predict what kinds of emergent properties would appear when animals begin interacting as part of a brain-net. In theory, you could imagine that a combination of brains could provide solutions that individual brains cannot achieve by themselves.

That sounds far-fetched. But Nicolelis’ lab is developing quite the track record of “taking science fiction and turning it into science,” says Ron Frostig, a neurobiologist at UC-Irvine who was not involved in the rat study. “He’s the most imaginative neuroscientist right now.” (Frostig made it clear he meant this as a complement, though skeptics might interpret the word less charitably.)

The most extensive coverage I’ve given Nicolelis and his work (including the Walk Again project) was in a March 16, 2012 post titled, Monkeys, mind control, robots, prosthetics, and the 2014 World Cup (soccer/football), although there are other mentions including in this Oct. 6, 2011 posting titled, Advertising for the 21st Century: B-Reel, ‘storytelling’, and mind control.  By the way, Nicolelis hopes to have a paraplegic individual (using technology Nicolelis is developing for the Walk Again project) kick the opening soccer/football to the 2014 World Cup games in Brazil.

While there’s much excitement about Nicolelis and his work, there are other ‘brain’ projects being developed in the US including the Brain Activity Map (BAM), which James Lewis notes in his Mar. 1, 2013 posting on the Foresight Institute blog,

A proposal alluded to by President Obama in his State of the Union address [Feb. 2013] to construct a dynamic “functional connectome” Brain Activity Map (BAM) would leverage current progress in neuroscience, synthetic biology, and nanotechnology to develop a map of each firing of every neuron in the human brain—a hundred billion neurons sampled on millisecond time scales. Although not the intended goal of this effort, a project on this scale, if it is funded, should also indirectly advance efforts to develop artificial intelligence and atomically precise manufacturing.

As Lewis notes in his posting, there’s an excellent description of BAM and other brain projects, as well as a discussion about how these ideas are linked (not necessarily by individuals but by the overall direction of work being done in many labs and in many countries across the globe) in Robert Blum’s Feb. (??), 2013 posting titled, BAM: Brain Activity Map Every Spike from Every Neuron, on his eponymous blog. Blum also offers an extensive set of links to the reports and stories about BAM. From Blum’s posting,

The essence of the BAM proposal is to create the technology over the coming decade
to be able to record every spike from every neuron in the brain of a behaving organism.
While this notion seems insanely ambitious, coming from a group of top investigators,
the paper deserves scrutiny. At minimum it shows what might be achieved in the future
by the combination of nanotechnology and neuroscience.

In 2013, as I write this, two European Flagship projects have just received funding for
one billion euro each (1.3 billion dollars each). The Human Brain Project is
an outgrowth of the Blue Brain Project, directed by Prof. Henry Markram
in Lausanne, which seeks to create a detailed simulation of the human brain.
The Graphene Flagship, based in Sweden, will explore uses of graphene for,
among others, creation of nanotech-based supercomputers. The potential synergy
between these projects is a source of great optimism.

The goal of the BAM Project is to elaborate the functional connectome
of a live organism: that is, not only the static (axo-dendritic) connections
but how they function in real-time as thinking and action unfold.

The European Flagship Human Brain Project will create the computational
capability to simulate large, realistic neural networks. But to compare the model
with reality, a real-time, functional, brain-wide connectome must also be created.
Nanotech and neuroscience are mature enough to justify funding this proposal.

I highly recommend reading Blum’s technical description of neural spikes as understanding that concept or any other in his post doesn’t require an advanced degree. Note: Blum holds a number of degrees and diplomas including an MD (neuroscience) from the University of California at San Francisco and a PhD in computer science and biostatistics from California’s Stanford University.

The Human Brain Project has been mentioned here previously. The  most recent mention is in a Jan. 28, 2013 posting about its newly gained status as one of two European Flagship initiatives (the other is the Graphene initiative) each meriting one billion euros of research funding over 10 years. Today, however, is the first time I’ve encountered the BAM project and I’m fascinated. Luckily, John Markoff’s Feb. 17, 2013 article for The New York Times provides some insight into this US initiative (Note: I have removed some links),

The Obama administration is planning a decade-long scientific effort to examine the workings of the human brain and build a comprehensive map of its activity, seeking to do for the brain what the Human Genome Project did for genetics.

The project, which the administration has been looking to unveil as early as March, will include federal agencies, private foundations and teams of neuroscientists and nanoscientists in a concerted effort to advance the knowledge of the brain’s billions of neurons and gain greater insights into perception, actions and, ultimately, consciousness.

Moreover, the project holds the potential of paving the way for advances in artificial intelligence.

What I find particularly interesting is the reference back to the human genome project, which may explain why BAM is also referred to as a ‘connectome’.

ETA Mar.6.13: I have found a Human Connectome Project Mar. 6, 2013 news release on EurekAlert, which leaves me confused. This does not seem to be related to BAM, although the articles about BAM did reference a ‘connectome’. At this point, I’m guessing that BAM and the ‘Human Connectome Project’ are two related but different projects and the reference to a ‘connectome’ in the BAM material is meant generically.  I previously mentioned the Human Connectome Project panel discussion held at the AAAS (American Association for the Advancement of Science) 2013 meeting in my Feb. 7, 2013 posting.

* Corrected EurkAlert to EurekAlert on June 14, 2013.