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References and links

References in related scientific subject areas:

SIM: Substrate-independent Minds

Foundations: Pattern survival versus Gene survival (Randal A. Koene)

Foundations: Substrate-Independent Minds (Randal A. Koene)

Foundations: A Window of Opportunity (Randal A. Koene)

SIM: Whole Brain Emulation

Koene, R.A. (2012). Fundamentals of Whole Brain Emulation: State, Transition and Update Representations, Special Issue of the International Journal on Machine Consciousness, Vol.4, No.1, (pre-print):

Koene, R.A. (2012). Experimental Research in Whole Brain Emulation: The Need for Innovative In-Vivo Measurement TechniquesSpecial Issue of the International Journal on Machine Consciousness, Vol.4, No.1, (pre-print):

Whole Brain Emulation: Roadmap (v1.0, 2007-2008, Future of Humanity Institute)

The Society of Neural Prosthetics and Whole Brain Emulation Science:

The Neural Prostheses Foundation investigating Transfer of Functions of the Mind: NeuralProstheses.Org

National Acadamy of Engineering's 14 "Grand Challenges for Engineering"Reverse-engineer the brain

Neuroscience: Large-Scale High-Resolution Brain Simulation and Neuroinformatics

Kozloski, J. and Wagner, J. (2011). An Ultrascalable Solution to Large-scale Neural Tissue Simulation, Frontiers in Neuroinformatics, Vol. 5, No.15, doi: 10.3389/fninf.2011.00015:

Parker, A.C., Friesz, A.K., and Pakdaman, A. (2006). Towards a Nanoscale Artificial Cortex, presented at The 2006 International Conference on Computing in Nanotechnology (CNAN'06), June 26-29, 2006, Las Vegas, USA:

BlueBrain project (Henry Markram)

NeuroModeling Geometric Reconstruction project: (Computational Visualization Center, Institute for Computational Engineering and Sciences, University of Texas at Austin)

Multi-Scale Object Oriented Simulation Environment (MOOSE): (Upinder S. Bhalla)

R. Appali, U. van Rienen and T. Heimburg. (2012). A comparison of the Hodgkin-Huxley model and the soliton theory for the action potential in nerves. Advances in Planar Lipid Bilayers and Liposomes 16: 275-299:

Neuroscience: Large-Scale High-Resolution Brain Data Acquisition and Connectomics

Marblestone, A.H., Bradley M. Zamft, Yael G. Maguire, Mikhail G. Shapiro, Thaddeus R. Cybulski, Joshua I. Glaser, Ben Stranges, Reza Kalhor, David A. Dalrymple, Dongjin Seo, Elad Alon, Michel M. Maharbiz, Jose Carmena, Jan Rabaey, Edward S. Boyden, George M. Church, Konrad P. Kording. (2013). Physical Principles for Scalable Neural Recording, Frontiers in Computational Neuroscience, 7:137. doi: 10.3389/fncom.2013.00137;;

Adam H Marblestone, Evan R Daugharthy, Reza Kalhor, Ian Peikon, Justus Kebschull, Seth L Shipman, Yuriy Mishchenko, David A Dalrymple, Bradley M Zamft, Konrad P Kording, Edward S Boyden, Anthony M Zador, George M Church. (2013). Conneconomics: The Economics of Large-Scale Neural Connectomics, bioRxiv, doi: 10.1101/001214:

Thaddeus R. Cybulski, Joshua I. Glaser, Adam H. Marblestone, Bradley M. Zamft, Edward S. Boyden, George M. Church, Konrad P. Kording. (2014). Spatial Information in Large-Scale Neural RecordingsarXiv:1402.3375 [q-bio.NC]:

Dongjin Seo, Jose M. Carmena, Jan M. Rabaey, Elad Alon, Michel M. Maharbiz. (2013). Neural Dust: An Ultrasonic, Low Power Solution for Chronic Brain-Machine Interfaces, arXiv:1307.2196 [q-bio.NC]:

Whole-Brain Ultrastructural Mapping: (Shawn Mikula)

Mouse Brain Architecture Project: (Partha Mitra)

KESM: (Yoonsuck Choe, Todd Huffman)

Knife-Edge Scanning Microscope Brain Atlas:

Osten, P. and Margrie, T.W. (2013). Mapping Brain Circuitry with a Light Microscope, Nature Methods, Vol.10(6), 515-523, doi:10.1038/NMETH.2477:

Human Connectome Project:

Open Connectome Project: Whole-Brain Circuit Reconstruction project web site: (Shawn Mikula)

Briggman, K.L., Helmstaedter, M., and Denk, W. (2011). Wiring Specificity in the Direction-Selectivity circuit of the retina, Nature, Vol.471, 183-188:

Bock, D.D., Lee, W.-C.A., Kerlin, A.M., Andermann, M.L., Hood, G., Wetzel, A.W., Yurgenson, S., Soucy, E.R., Kim, H.S., and Reid, R.C. (2011). Network anatomy and in vivo physiology of visual cortical neurons, Nature, Vol.471, 177-182:

Andres, B., Koethe, U., Kroeger, T., Helmstaedter, M., Briggman, K.L., Denk, W. and Hamprecht, F.A. (2012).  3D Segmentation of SBFSEM Images of Neuropil by a Graphical Model of Supervoxel Boundaries, Medical Image Analysis, Vol.16(4), 796-805, doi:10.1016/ (contact for a PDF of the full article)

Alivisatos, A.P., Chun, M., Church, G.M., Greenspan, R.J., Roukes, M.L. and Yuste, R. (2012). The Brain Activity Map Project and the Challenge of Functional Connectomics, Neuron, Vol. 74(6), 970-974. doi:10.1016/j.neuron.2012.06.006:

Kording, K.P. (2011). Of toasters and molecular ticker tapesPLoS Computational Biology, Vol. 7(12): e1002291. doi:10.1371/journal.pcbi.1002291:

Stevenson, I.H., Kording, K.P. (2011). How advances in neural recording affect data analysis, Nature Neuroscience, Vol.14(2), 139-142:

Synthetic Neurobiology Group: (Ed Boyden)

WormBase: (and mirror site

White, J.G., Southgate, E., Thomson, J.N., and Brenner, S., F.R.S. (1986). The Structure of the Nervous System of the Nematode Caenorhabditis Elegans, Phil. Trans. Royal Soc. London. Series B, Biol Scien. Vol.314, Issue 1165, 1-340:

SFN BrainFacts:

Cracking the Neural Code, Third Annual Aspen Brain Forum (2012), Slides and Audio provided in the "Media" section:

The Virtual Brain Project:

Neuroscience: Neural Engineering (Ted Berger)
and the Center for Neural Engineering, Theodore W. Berger Labs at USC:

BrainGate project: (John Donoghue)

Gómez-Martínez, R., Vázquez, P., Duch, M., Muriano, A., Pinacho, D., Sanvicens, N., Sánchez-Baeza, F., Boya, P., de la Rosa, E. J., Esteve, J., Suárez, T. and Plaza, J. A. (2010), Intracellular Silicon Chips in Living Cells. Small, 6: 499–502. doi: 10.1002/smll.200901041:

Computing Devices: Neuromimetics

The BioRC Biomimetic Real-Time Cortex Project (Alice Parker)
and summary on building brain emulation platforms: Challenges for Brain Emulation: Why is Building a Brain so Difficult? (Rick Cattell & Alice Parker)

AI: Artificial General Intelligence

Foundations: Pavlov's AI - What did it mean? (Suzanne Gildert)

Bérut A, Arakelyan A, Petrosyan A, Ciliberto S, Dillenschneider R, Lutz E. (2012). Experimental verification of Landauer's principle linking information and thermodynamicsNature. 2012 Mar 7;483(7388):187-9. doi: 10.1038/nature10872:

Philip Ball (2012). The unavoidable cost of computation revealed. Physicists have proved that forgetting is the undoing of Maxwell’s demon. Nature doi:10.1038/nature.2012.10186:


ALCOR (Scottsdale, Arizona)

Philosophy of Mind: Consciousness

Rick Grush and Patricia Smith Churchland (1995). Gaps in Penrose's toilings, Journal of Consciousness Studies, Vol.2, Issue 1, 10-29:

Philosophy of Mind
: Qualia

Carroll, J. (2012). Epiphenomenalism, the Problem with Property Dualism. Presented this paper at the 2012 Conference of the Mormon Transhumanist Association