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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)

Keith Wiley and Randal A. Koene (2015). The Fallacy of Favoring Gradual Replacement Mind Uploading Over Scan-and-Copy. (Preprint). Also available as PDF.

Keith Wiley (2014). A Taxonomy and Metaphysics of Mind-UploadingHumanity+ Press and Alautun Press.

Blackford, R. and Broderick, D. (Eds.) (2014). Intelligence Unbound: The Future of Uploaded and Machine Minds, Wiley-Blackwell, Oxford, UK, pre-print of contributed chapter by Koene, R.A.: Feasible Mind Uploading, original title: System Identification: The foundation of modern science and the core of feasible mind uploading

SIM: Whole Brain Emulation

Koene, R.A and Deca, D. (Eds.) (2013). Brain Emulation and Connectomics: a Convergence of Neuroscience and Artificial General Intelligence, Special Issue of the Journal of Artificial General Intelligence, Vol.4, No.3, doi:10.2478/jagi-2013-0005 to doi:10.2478/jagi-2013-0012:

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

Lee, Wei-Chung Allen and Bonin, Vincent and Reed, Michael and Graham, Brett J. and Hood, Greg and Glattfelder, Katie and Reid, R. Clay. (2016). Anatomy and function of an excitatory network in the visual cortex, Nature, doi: 10.1038/nature17192:, ( content sharing initiative online access to full article)

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

Tim Dettmers. (2015). The Brain vs Deep Learning Part I: Computational Complexity — Or Why the Singularity Is Nowhere Near

Neurokernel: An open source platform for emulating the fruit fly brain: (Aurel Lazar)

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

Shawn Mikula. (2016). Progress Towards Mammalian Whole-Brain Cellular Connectomics, Frontiers in Neuroanatomy

Robert L. McIntyre and Gregory M. Fahy. (2015). Aldehyde-stabilized cryopreservationCryobiology, doi:

Samuel G. Rodriques, Adam H. Marblestone, Max Mankin, Lowell Wood, Edward
Boyden. (2013). Multiplexed Neural Recording Down a Single Optical Fiber via
Optical Reflectometry with Capacitive Signal Enhancement, arXiv:1506.01033

Narayanan Kasthuri, Kenneth Jeffrey Hayworth, Daniel Raimund Berger, Richard Lee Schalek, José Angel Conchello, Seymour Knowles-Barley, Dongil Lee, Amelio Vázquez-Reina, Verena Kaynig, Thouis Raymond Jones, Mike Roberts, Josh Lyskowski Morgan, Juan Carlos Tapia, H. Sebastian Seung, William Gray Roncal, Joshua Tzvi Vogelstein, Randal Burns, Daniel Lewis Sussman, Carey Eldin Priebe, Hanspeter Pfister, Jeff William Lichtman. (2015). Saturated Reconstruction of a Volume of Neocortex, Cell, Volume 162, Issue 3, p648–661, 30 July 2015. DOI:
With video:

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:

Adam H Marblestone, Evan R Daugharthy, Reza Kalhor, Ian D Peikon, Justus M Kebschull, Seth L Shipman, Yuriy Mishchenko, Je Hyuk Lee, Konrad P Kording, Edward S Boyden, Anthony M Zador, George M Church. (2014). Rosetta Brains: A Strategy for Molecularly-Annotated ConnectomicsarXiv:1404.5103 [q-bio.NC]:

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]:

Daniel R Hochbaum, Yongxin Zhao, Samouil L Farhi, Nathan Klapoetke, Christopher A Werley, Vikrant Kapoor, Peng Zou, Joel M Kralj, Dougal Maclaurin, Niklas Smedemark-Margulies, Jessica L Saulnier, Gabriella L Boulting, Christoph Straub, Yong Ku Cho, Michael Melkonian, Gane Ka-Shu Wong, D Jed Harrison, Venkatesh N Murthy, Bernardo L Sabatini, Edward S Boyden, Robert E Campbell & Adam E Cohen. (2014). All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins, Nature Methodsdoi:10.1038/nmeth.3000:

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E.S. Boyden, A. Vaziri. (2014). Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy, Nature Methods, doi:10.1038/nmeth.2964:

James Kunert, Eli Shlizerman, J. Nathan Kutz. (2014). Low-dimensional functionality of complex network dynamics: Neurosensory integration in the Caenorhabditis elegans connectome, Physical Review E, 89, 052805, DOI:

Briggman, K.L., Helmstaedter, M., and Denk, W. (2011). Wiring Specificity in the Direction-Selectivity circuit of the retinaNature, 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 neuronsNature, 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 BoundariesMedical Image Analysis, Vol.16(4), 796-805, doi:10.1016/ (contact for a PDF of the full article)

Alivisatos AP1, Andrews AM, Boyden ES, Chun M, Church GM, Deisseroth K, Donoghue JP, Fraser SE, Lippincott-Schwartz J, Looger LL, Masmanidis S, McEuen PL, Nurmikko AV, Park H, Peterka DS, Reid C, Roukes ML, Scherer A, Schnitzer M, Sejnowski TJ, Shepard KL, Tsao D, Turrigiano G, Weiss PS, Xu C, Yuste R, Zhuang X. (2013). Nanotools for neuroscience and brain activity mapping. ACS Nano. Mar 26;7(3):1850-66. doi: 10.1021/nn4012847. Epub 2013 Mar 20:

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 ConnectomicsNeuron, Vol. 74(6), 970-974. doi:10.1016/j.neuron.2012.06.006:

Eric Jonas and Konrad Kording. (2014). Automatic discovery of cell types and microcircuitry from neural connectomicsarXiv:1407.4137:

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 analysisNature Neuroscience, Vol.14(2), 139-142:

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

Varshney LR, Chen BL, Paniagua E, Hall DH, Chklovskii DB. (2011). Structural Properties of the Caenorhabditis elegans Neuronal Network. PLoS Computational Biology, 7(2): e1001066. doi:10.1371/journal.pcbi.1001066:

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:

Expansion Microscopy: (Boyden lab)

Whole-Brain Ultrastructural Mapping: (Shawn Mikula)

Mouse Brain Architecture Project: (Partha Mitra)

KESM: (Yoonsuck Choe, Todd Huffman)

Knife-Edge Scanning Microscope Brain Atlas:

Human Connectome Project:

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

Synthetic Neurobiology Group: (Ed Boyden)

SFN BrainFacts:

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

The Virtual Brain Project:

: Neural Engineering

Hippocampal Prosthesis: (Ted Berger) [link may be outdated]
and the Center for Neural Engineering, Theodore W. Berger Labs at USC:

Berger, T. W., Song, D., Chan, R. H. M., Marmarelis, V. Z., LaCoss, J., Wills, J., Hampson, R.E., Deadwyler, S.A., Granacki, J. J. (2012). A Hippocampal Cognitive Prosthesis: Multi-Input, Multi-Output Nonlinear Modeling and VLSI ImplementationIeee Transactions on Neural Systems and Rehabilitation Engineering20(2), 198–211.

Herreros, I. and Giovannucci, A. and Taub, A.H. and Hogri, R. and Magal, A. and Bamford, S. and Pruecki, R. and Verschure, P.F.M.J. (2014). A cerebellar neuroprosthetic system: computational architecture and in vivo testFrontiers in Bioengineering and Biotechnology, Vol.2:14, doi: doi:10.3389/fbioe.2014.00014:

David J. Guggenmosa, Meysam Azinc, Scott Barbaya, Jonathan D. Mahnkend, Caleb Dunhama, Pedram Mohsenic, and Randolph J. Nudo. (2013). Restoration of function after brain damage using a neural prosthesis, Proceedings of the National Academy of Sciences, Vol.110, No.52, pp. 21177–21182, doi: 10.1073/pnas.1316885110:

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 CellsSmall, 6: 499–502. doi: 10.1002/smll.200901041:

Deca, D. and Koene, R.A. (2014). Experimental enhancement of neurphysiological functionFrontiers in Systems Neuroscience, Vol. 8: 189, doi: 10.3389/fnsys.2014.00189:

Chris Eliasmith, Charles H. Anderson

Neuroscience: Basics

Nicolas Brunel, Vincent Hakim and Magnus JE Richardson. (2014). Single neuron dynamics and computationCurrent Opinion in Neurobiology, April 2014, Pages 149–155:

Koch, C. and Marcus, G. (2014). Cracking the Brain’s Codes: How does the brain speak to itself?, MIT Technology Review, June 17:

Eric R. Kandel,
James H. Schwartz,
Thomas M. Jessell,
Steven A. Siegelbaum,
A. J. Hudspeth

Thomas J. Anastasio

Christof Koch

Roland Baddeley, Peter Hancock, Peter Földiák

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)

Computing DevicesNeuromorphic Systems

Jennifer Hasler and Bo Marr (2013). Finding a roadmap to achieve large neuromorphic hardware systems. Frontiers in Neuroscience, Vol. 7, Article 118. doi: 10.3389/fnins.2013.00118

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

Abninder Litta, Chris Eliasmith, Frederick W. Kroona, Steven Weinstein, and Paul Thagarda (2006). Is the Brain a Quantum Computer? Cognitive Science, Vol.30, 593-603.

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