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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)





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: http://carboncopies.org/call-for-papers-jagi-special-issue-on-brain-emulation-and-connectomics-a-convergence-of-neuroscience-and-artificial-general-intelligence

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): http://carboncopies.org/research-projects/articles-and-essays/koene.IJMC.fundamentals-of-WBE-state-transition-and-update-representations.proofs-20120410.pdf

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): http://carboncopies.org/research-projects/articles-and-essays/koene.IJMC.experimental-research-in-WBE-the-need-for-innovative-in-vivo-measurement-techniques.proofs-20120410.pdf

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

The Society of Neural Prosthetics and Whole Brain Emulation Science: minduploading.org

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: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175572/

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: http://eve.usc.edu/Publications/NanoscaleArtificialCortex.pdf

BlueBrain projecthttp://bluebrain.epfl.ch/ (Henry Markram)

NeuroModeling Geometric Reconstruction project: http://cvcweb.ices.utexas.edu/cvcwp/?page_id=176 (Computational Visualization Center, Institute for Computational Engineering and Sciences, University of Texas at Austin)

Multi-Scale Object Oriented Simulation Environment (MOOSE): http://moose.sourceforge.net/ (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: http://www.membranes.nbi.dk/pdf/2012_AppalivanRienenHeimburg_APLBL.pdf

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; http://journal.frontiersin.org/Journal/10.3389/fncom.2013.00137/abstract;

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: http://biorxiv.org/content/early/2013/12/16/001214

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]: http://arxiv.org/abs/1404.5103

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]: http://arxiv.org/abs/1402.3375

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]: http://arxiv.org/abs/1307.2196

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: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3000.html?message-global=remove

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: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2964.html

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: http://dx.doi.org/10.1103/PhysRevE.89.052805

Briggman, K.L., Helmstaedter, M., and Denk, W. (2011). Wiring Specificity in the Direction-Selectivity circuit of the retinaNature, Vol.471, 183-188: http://www.nature.com/nature/journal/v471/n7337/full/nature09818.html

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: http://www.nature.com/nature/journal/v471/n7337/full/nature09802.html

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/j.media.2011.11.004: http://www.sciencedirect.com/science/article/pii/S1361841511001666 (contact rak@carboncopies.org 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 ConnectomicsNeuron, Vol. 74(6), 970-974. doi:10.1016/j.neuron.2012.06.006: http://www.cell.com/neuron/abstract/S0896-6273(12)00518-1

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

Kording, K.P. (2011). Of toasters and molecular ticker tapesPLoS Computational Biology, Vol. 7(12): e1002291. doi:10.1371/journal.pcbi.1002291: http://klab.smpp.northwestern.edu/wiki/images/7/7d/Kording_Toaster_Molecular_Ticket_Tapes_2011.pdf

Stevenson, I.H., Kording, K.P. (2011). How advances in neural recording affect data analysisNature Neuroscience, Vol.14(2), 139-142: http://klab.wikidot.com/local--files/ian-stevenson/nn.2731.pdf

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: http://www.nature.com/nmeth/journal/v10/n6/pdf/nmeth.2477.pdf

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: http://www.wormatlas.org/ver1/MoW_built0.92/toc.html

Whole-Brain Ultrastructural Mapping: http://homes.mpimf-heidelberg.mpg.de/~smikula/blockface/ (Shawn Mikula)

Mouse Brain Architecture Project: http://brainarchitecture.org/ (Partha Mitra)



KESM: http://research.cs.tamu.edu/bnl/kesm.html (Yoonsuck Choe, Todd Huffman)

Knife-Edge Scanning Microscope Brain Atlas: http://kesm.cs.tamu.edu/

Human Connectome Project: http://www.humanconnectomeproject.org


Open Connectome Project: http://openconnectomeproject.org

Connectomes.org Whole-Brain Circuit Reconstruction project web site: connectomes.org (Shawn Mikula)


Synthetic Neurobiology Group: http://syntheticneurobiology.org/ (Ed Boyden)

SFN BrainFacts: http://brainfacts.org

Cracking the Neural Code, Third Annual Aspen Brain Forum (2012), Slides and Audio provided in the "Media" section: http://www.nyas.org/Publications/Ebriefings/Detail.aspx?cid=bd737d49-01a9-49b2-a337-681146892540

The Virtual Brain Project: http://thevirtualbrain.org

Neuroscience
: Neural Engineering

Neural-Prosthesis.com: http://www.neural-prosthesis.com/ (Ted Berger)
and the Center for Neural Engineering, Theodore W. Berger Labs at USC: http://cne.usc.edu/

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: http://www.pnas.org/content/110/52/21177.full

BrainGate projecthttp://www.braingate2.org/ (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: http://onlinelibrary.wiley.com/doi/10.1002/smll.200901041/abstract


Chris Eliasmith, Charles H. Anderson







Neuroscience: Basics

Koch, C. and Marcus, G. (2014). Cracking the Brain’s Codes: How does the brain speak to itself?, MIT Technology Review, June 17: http://www.technologyreview.com/featuredstory/528131/cracking-the-brains-codes/


Editors:
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 Projecthttp://ceng.usc.edu/~parker/BioRC_research.html (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.2013.00118http://journal.frontiersin.org/Journal/10.3389/fnins.2013.00118/full

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: http://www.nature.com/nature/journal/v483/n7388/full/nature10872.html

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: http://www.nature.com/news/the-unavoidable-cost-of-computation-revealed-1.10186

Cryonics

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: http://mind.ucsd.edu/papers/penrose/penrosehtml/penrose-text.html

Philosophy of Mind
: Qualia

Carroll, J. (2012). Epiphenomenalism, the Problem with Property Dualism. Presented this paper at the 2012 Conference of the Mormon Transhumanist Associationhttp://www.scribd.com/doc/133477927/Epiphenominalism-and-the-Problem-with-Property-Dualism-by-James-Carroll

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