Re-membering the body: Applications of computational neuroscience to the top-down control of regeneration of limbs and other complex organs

Integrative Biology (United Kingdom)

Volumn 7, Issue 12, 2015, Pages 1487-1517

  Pezzulo, G ^a   Levin, M ^b  

^a INSTITUTE OF COGNITIVE SCIENCES AND TECHNOLOGIES   (Italy)

^b TUFTS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOENERGY; BIOENGINEERING; BRAIN NERVE CELL; CELL FUNCTION; CELL STRUCTURE; CENTRAL NERVOUS SYSTEM; COGNITION; DECISION MAKING; DEVELOPMENTAL BIOLOGY; HUMAN; INFORMATION PROCESSING; LIMB REGENERATION; MEMORY; MORPHOGENESIS; NEUROSCIENCE; PRIORITY JOURNAL; REGENERATIVE MEDICINE; REVIEW; SIGNAL TRANSDUCTION; ANIMAL; BIOLOGICAL MODEL; ELECTROPHYSIOLOGY; LIMB; PHYSIOLOGY; REGENERATION; SYNTHETIC BIOLOGY;

ANIMALS; BIOENGINEERING; BODY PATTERNING; COGNITION; DEVELOPMENTAL BIOLOGY; ELECTROPHYSIOLOGICAL PHENOMENA; EXTREMITIES; HUMANS; MODELS, BIOLOGICAL; MORPHOGENESIS; NEUROSCIENCES; REGENERATION; REGENERATIVE MEDICINE; SIGNAL TRANSDUCTION; SYNTHETIC BIOLOGY;

EID: 84948771063     PISSN: 17579694     EISSN: 17579708     Source Type: Journal    
DOI: 10.1039/c5ib00221d     Document Type: Review

References (265)

1. D. E. Ingber M. Levin What lies at the interface of regenerative medicine and developmental biology? Development 2007 134 2541 2547
2. C. L. Stoick-Cooper R. T. Moon G. Weidinger Advances in signaling in vertebrate regeneration as a prelude to regenerative medicine Genes Dev. 2007 21 1292 2315
3. R. D. Kamm R. Bashir Creating living cellular machines Ann. Biomed. Eng. 2014 42 445 459 10.1007/s10439-013-0902-7
4. V. French Positional information around the segments of the cockroach leg J. Embryol. Exp. Morphol. 1980 59 281 313
5. N. J. Oviedo P. A. Newmark A. Sanchez Alvarado Allometric scaling and proportion regulation in the freshwater planarian Schmidtea mediterranea Dev. Dyn. 2003 226 326 333
6. N. Farinella-Ferruzza The transformation of a tail into a limb after xenoplastic transformation Experientia 1956 15 304 305
7. L. N. Vandenberg D. S. Adams M. Levin Normalized shape and location of perturbed craniofacial structures in the Xenopus tadpole reveal an innate ability to achieve correct morphology Dev. Dyn. 2012 241 863 878 10.1002/dvdy.23770
8. D. Lobo M. Solano G. A. Bubenik M. Levin A linear-encoding model explains the variability of the target morphology in regeneration J. R. Soc., Interface 2014 11 20130918 10.1098/rsif.2013.0918
9. A. Reina G. Valentini C. Fernandez-Oto M. Dorigo V. Trianni A design pattern for decentralised decision making PLoS One 2015 10.1371/journal.pone.0140950
10. S. M. Rose H. M. Wallingford Transformation of renal tumors of frogs to normal tissues in regenerating limbs of salamanders Science 1948 107 457
11. K. Illmensee B. Mintz Totipotency and normal differentiation of single teratocarcinoma cells cloned by injection into blastocysts Proc. Natl. Acad. Sci. U. S. A. 1976 73 549 553
12. H. N. Chia B. M. Wu Recent advances in 3D printing of biomaterials J. Biol. Eng. 2015 9 4 10.1186/s13036-015-0001-4
13. S. V. Murphy A. Atala 3D bioprinting of tissues and organs Nat. Biotechnol. 2014 32 773 785 10.1038/nbt.2958
14. M. Levin The wisdom of the body: future techniques and approaches to morphogenetic fields in regenerative medicine, developmental biology and cancer Regener. Med. 2011 6 667 673 10.2217/rme.11.69
15. R. Doursat H. Sayama O. Michel A review of morphogenetic engineering Nat. Comput. 2013 12 517 535 10.1007/S11047-013-9398-1
16. C. J. Sheeba R. P. Andrade I. Palmeirim Limb Patterning: From Signaling Gradients to Molecular Oscillations J. Mol. Biol. 2014 426 780 784
17. S. Kim H. J. Kim N. L. Jeon Biological applications of microfluidic gradient devices Integr. Biol. 2010 2 584 603 10.1039/c0ib00055h
18. J. Slack Establishment of spatial pattern Wiley Interdiscip. Rev.: Dev. Biol. 2014 3 379 388
19. Y. Morishita K. Hironaka Systems approach to developmental biology-designs for robust patterning IET Syst. Biol. 2013 7 38 49
20. M. von Dassow L. A. Davidson Physics and the canalization of morphogenesis: a grand challenge in organismal biology Phys. Biol. 2011 8 045002 10.1088/1478-3975/8/4/045002
21. A. Mammoto T. Mammoto D. E. Ingber Mechanosensitive mechanisms in transcriptional regulation J. Cell Sci. 2012 125 3061 3073
22. E. Brouzes E. Farge Interplay of mechanical deformation and patterned gene expression in developing embryos Curr. Opin. Genet. Dev. 2004 14 367 374
23. F. Chang N. Minc Electrochemical control of cell and tissue polarity Annu. Rev. Cell Dev. Biol. 2014 30 317 336 10.1146/annurev-cellbio-100913-013357
24. L. V. Beloussov Morphogenesis can be driven by properly parametrised mechanical feedback Eur. Phys. J. E: Soft Matter Biol. Phys. 2013 36 132 10.1140/epje/i2013-13132-x
25. S. Stewart A. Rojas-Munoz J. C. Izpisua Belmonte Bioelectricity and epimorphic regeneration BioEssays 2007 29 1133 1137 10.1002/bies.20656
26. C. D. McCaig A. M. Rajnicek B. Song M. Zhao Controlling cell behavior electrically: current views and future potential Physiol. Rev. 2005 85 943 978
27. M. Levin Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo Mol. Biol. Cell 2014 25 3835 3850 10.1091/mbc.E13-12-0708
28. R. Doursat, H. Sayama, O. Michel, Morphogenetic Engineering: Reconciling Self-Organization and Architecture, Morphogenetic Engineering: Toward Programmable Complex Systems, 2012, pp. 1-24 10.1007/978-3-642-33902-8-1
29. A. Tseng M. Levin Cracking the bioelectric code: probing endogenous ionic controls of pattern formation Commun. Integr. Biol. 2013 6 1 8
30. M. Levin Reprogramming cells and tissue patterning via bioelectrical pathways: molecular mechanisms and biomedical opportunities Wiley Interdiscip. Rev.: Syst. Biol. Med. 2013 5 657 676 10.1002/wsbm.1236
31. M. Levin C. G. Stevenson Regulation of cell behavior and tissue patterning by bioelectrical signals: challenges and opportunities for biomedical engineering Annu. Rev. Biomed. Eng. 2012 14 295 323 10.1146/annurev-bioeng-071811-150114
32. M. Levin Endogenous bioelectrical networks store non-genetic patterning information during development and regeneration J. Physiol. 2014 592 2295 2305 10.1113/jphysiol.2014.271940
33. M. Levin Gap junctional communication in morphogenesis Prog. Biophys. Mol. Biol. 2007 94 186 206
34. A. E. Pereda S. Curti G. Hoge R. Cachope C. E. Flores J. E. Rash Gap junction-mediated electrical transmission: regulatory mechanisms and plasticity Biochim. Biophys. Acta 2013 1828 134 146 10.1016/j.bbamem.2012.05.026
35. S. Anava Y. Saad A. Ayali The role of gap junction proteins in the development of neural network functional topology Insect Mol. Biol. 2013 22 457 472
36. R. Cachope K. Mackie A. Triller J. O'Brien A. Pereda Potentiation of electrical and glutamatergic synaptic transmission mediated by endocannabinoids Neuron 2007 56 1034 1047
37. W. S. Mcculloch, in Cerebral Mechanisms in Behavior: The Hixon Symposium, ed., L. A. Jeffress, 1951, pp. 42-81
38. N. Palacios-Prado F. F. Bukauskas Heterotypic gap junction channels as voltage-sensitive valves for intercellular signaling Proc. Natl. Acad. Sci. U. S. A. 2009 106 14855 14860 10.1073/pnas.0901923106
39. M. Yang W. J. Brackenbury Membrane potential and cancer progression Front. Physiol. 2013 4 185 10.3389/fphys.2013.00185
40. A. Roberts C. A. Stirling Properties and Propagation of a Cardiac-Like Impulse in Skin of Young Tadpoles Z. Vgl. Physiol. 1971 71 295 310
41. L. N. Vandenberg D. J. Blackiston A. C. Rea T. M. Dore M. Levin Left-right patterning in Xenopus conjoined twin embryos requires serotonin signaling and gap junctions Int. J. Dev. Biol. 2014 58 799 809 10.1387/ijdb.140215ml
42. M. Levin M. Mercola Gap junction-mediated transfer of left-right patterning signals in the early chick blastoderm is upstream of Shh asymmetry in the node Development 1999 126 4703 4714
43. B. T. Chernet C. Fields M. Levin Long-range gap junctional signaling controls oncogene-mediated tumorigenesis in Xenopus laevis embryos Front. Physiol. 2015 5 519 10.3389/fphys.2014.00519
44. E. McLachlan Q. Shao H. L. Wang S. Langlois D. W. Laird Cancer Res. 2006 66 9886 9894
45. N. J. Oviedo J. Morokuma P. Walentek I. P. Kema M. B. Gu J. M. Ahn J. S. Hwang T. Gojobori M. Levin Long-range neural and gap junction protein-mediated cues control polarity during planarian regeneration Dev. Biol. 2010 339 188 199 10.1016/j.ydbio.2009.12.012
46. T. Nogi M. Levin Characterization of innexin gene expression and functional roles of gap-junctional communication in planarian regeneration Dev. Biol. 2005 287 314 335
47. Q. V. Ton M. K. Iovine Identification of an evx1-Dependent Joint-Formation Pathway during FIN Regeneration PLoS One 2013 8 e81240 10.1371/journal.pone.0081240
48. Q. V. Ton M. Kathryn Iovine Semaphorin3d mediates Cx43-dependent phenotypes during fin regeneration Dev. Biol. 2012 366 195 203 10.1016/j.ydbio.2012.03.020
49. D. S. Adams M. Levin Endogenous voltage gradients as mediators of cell-cell communication: strategies for investigating bioelectrical signals during pattern formation Cell Tissue Res. 2013 352 95 122 10.1007/s00441-012-1329-4
50. D. S. Adams M. Levin General principles for measuring resting membrane potential and ion concentration using fluorescent bioelectricity reporters Cold Spring Harbor Protoc. 2012 2012 385 397 10.1101/pdb.top067710
51. W. Akemann H. Mutoh A. Perron Y. Kyung Park Y. Iwamoto T. Knopfel Imaging Neural Circuit Dynamics with a Voltage-Sensitive Fluorescent Protein J. Neurophysiol. 2012 108 2323 2337
52. D. S. Adams M. Levin Measuring resting membrane potential using the fluorescent voltage reporters DiBAC4(3) and CC2-DMPE Cold Spring Harbor Protoc. 2012 2012 459 464 10.1101/pdb.prot067702
53. N. J. Oviedo C. L. Nicolas D. S. Adams M. Levin Live Imaging of Planarian Membrane Potential Using DiBAC4(3) Cold Spring Harbor Protoc. 2008 10.1101/pdb.prot5055
54. V. P. Pai J. M. Lemire J. F. Pare G. Lin Y. Chen M. Levin Endogenous Gradients of Resting Potential Instructively Pattern Embryonic Neural Tissue via Notch Signaling and Regulation of Proliferation J. Neurosci. 2015 35 4366 4385 10.1523/jneurosci.1877-14.2015
55. D. S. Adams A. S. Tseng M. Levin Biol. Open 2013 2 306 313 10.1242/bio.20133665
56. N. Ozkucur H. H. Epperlein R. H. Funk Ion imaging during axolotl tail regeneration in vivo Dev. Dyn. 2010 239 2048 2057 10.1002/dvdy.22323
57. V. P. Pai S. Aw T. Shomrat J. M. Lemire M. Levin Transmembrane voltage potential controls embryonic eye patterning in Xenopus laevis Development 2012 139 313 323 10.1242/dev.073759
58. S. Park R. A. Koppes U. P. Froriep X. Jia A. K. Achyuta B. L. McLaughlin P. Anikeeva Optogenetic control of nerve growth Sci. Rep. 2015 5 9669 10.1038/srep09669
59. L. Fenno O. Yizhar K. Deisseroth The development and application of optogenetics Annu. Rev. Neurosci. 2011 34 389 412 10.1146/annurev-neuro-061010-113817
60. D. S. Adams J. M. Lemire R. H. Kramer M. Levin Optogenetics in Developmental Biology: using light to control ion flux-dependent signals in Xenopus embryos Int. J. Dev. Biol. 2014 58 851 861 10.1387/ijdb.140207ml
61. A. Haupt A. Campetelli D. Bonazzi M. Piel F. Chang N. Minc Electrochemical regulation of budding yeast polarity PLoS Biol. 2014 12 e1002029 10.1371/journal.pbio.1002029
62. W. S. Beane J. Morokuma D. S. Adams M. Levin A Chemical genetics approach reveals H,K-ATPase-mediated membrane voltage is required for planarian head regeneration Chem. Biol. 2011 18 77 89
63. D. J. Blackiston G. M. Anderson N. Rahman C. Bieck M. Levin A Novel Method for Inducing Nerve Growth via Modulation of Host Resting Potential: Gap Junction-Mediated and Serotonergic Signaling Mechanisms Neurotherapeutics 2015 12 170 184 10.1007/s13311-014-0317-7
64. D. Blackiston D. S. Adams J. M. Lemire M. Lobikin M. Levin Transmembrane potential of GlyCl-expressing instructor cells induces a neoplastic-like conversion of melanocytes via a serotonergic pathway Dis. Models & Mech. 2011 4 67 85 10.1242/dmm.005561
65. D. S. Adams K. R. Robinson T. Fukumoto S. Yuan R. C. Albertson P. Yelick L. Kuo M. McSweeney M. Levin Early, H + -V-ATPase-dependent proton flux is necessary for consistent left-right patterning of non-mammalian vertebrates Development 2006 133 1657 1671
66. A. S. Tseng M. Levin Transducing bioelectric signals into epigenetic pathways during tadpole tail regeneration Anat. Rec. 2012 295 1541 1551 10.1002/ar.22495
67. B. T. Chernet M. Levin Transmembrane voltage potential is an essential cellular parameter for the detection and control of tumor development in a Xenopus model Dis. Models & Mech. 2013 6 595 607 10.1242/dmm.010835
68. B. T. Chernet M. Levin Transmembrane voltage potential of somatic cells controls oncogene-mediated tumorigenesis at long-range Oncotarget 2014 5 3287 3306
69. Y. Okamura J. E. Dixon Voltage-sensing phosphatase: its molecular relationship with PTEN Physiology 2011 26 6 13 10.1152/physiol.00035.2010
70. J. Lacroix C. R. Halaszovich D. N. Schreiber M. G. Leitner F. Bezanilla D. Oliver C. A. Villalba-Galea Controlling the activity of a phosphatase and tensin homolog (PTEN) by membrane potential J. Biol. Chem. 2011 286 17945 17953 10.1074/jbc.M110.201749
71. Y. Murata H. Iwasaki M. Sasaki K. Inaba Y. Okamura Phosphoinositide phosphatase activity coupled to an intrinsic voltage sensor Nature 2005 435 1239 1243
72. Y. Zhou C. O. Wong K. J. Cho D. van der Hoeven H. Liang D. P. Thakur J. Luo M. Babic K. E. Zinsmaier M. X. Zhu H. Hu K. Venkatachalam J. F. Hancock Signal Transduction. Membrane potential modulates plasma membrane phospholipid dynamics and K-Ras signaling Science 2015 349 873 876 10.1126/science.aaa5619
73. R. Binggeli R. Weinstein Membrane potentials and sodium channels: hypotheses for growth regulation and cancer formation based on changes in sodium channels and gap junctions J. Theor. Biol. 1986 123 377 401
74. M. Levin Molecular bioelectricity in developmental biology: new tools and recent discoveries: control of cell behavior and pattern formation by transmembrane potential gradients BioEssays 2012 34 205 217 10.1002/bies.201100136
75. K. M. O'Connell A. S. Rolig J. D. Whitesell M. M. Tamkun Kv2.1 potassium channels are retained within dynamic cell surface microdomains that are defined by a perimeter fence J. Neurosci. 2006 26 9609 9618 10.1523/jneurosci.1825-06.2006
76. J. D. Victor Temporal aspects of neural coding in the retina and lateral geniculate Network 1999 10 R1 R66
77. N. Ozkucur K. P. Quinn J. C. Pang C. Du I. Georgakoudi E. Miller M. Levin D. L. Kaplan Membrane potential depolarization causes alterations in neuron arrangement and connectivity in cocultures Brain Behav. 2015 5 24 38 10.1002/brb3.295
78. S. Sundelacruz C. Li Y. J. Choi M. Levin D. L. Kaplan Bioelectric modulation of wound healing in a 3D in vitro model of tissue-engineered bone Biomaterials 2013 34 6695 6705 10.1016/j.biomaterials.2013.05.040
79. S. Sundelacruz M. Levin D. L. Kaplan Depolarization alters phenotype, maintains plasticity of predifferentiated mesenchymal stem cells Tissue Eng., Part A 2013 19 1889 1908 10.1089/ten.tea.2012.0425.rev
80. S. Sundelacruz M. Levin D. L. Kaplan Membrane potential controls adipogenic and osteogenic differentiation of mesenchymal stem cells PLoS One 2008 3 e3737
81. S. Sundelacruz M. Levin D. L. Kaplan Role of membrane potential in the regulation of cell proliferation and differentiation Stem Cell Rev. Rep. 2009 5 231 246
82. M. H. You M. S. Song S. K. Lee P. D. Ryu S. Y. Lee D. Y. Kim Voltage-gated K(+) channels in adipogenic differentiation of bone marrow-derived human mesenchymal stem cells. Acta Pharmacol. Sin. 2013 34 129 136
83. J.-Y. Lan C. Williams M. Levin L. Black III Depolarization of Cellular Resting Membrane Potential Promotes Neonatal Cardiomyocyte Proliferation In Vitro Cell. Mol. Bioeng. 2014 1 14 10.1007/s12195-014-0346-7
84. P. Jiang S. Rushing C. W. Kong J. Fu D. K. Lieu C. Chan W. Deng R. Li Electrophysiological Properties of Human Induced Pluripotent Stem Cells Am. J. Physiol.: Cell Physiol. 2010 298 C486 C495
85. X. Jia J. Yang W. Song P. Li X. Wang C. Guan L. Yang Y. Huang X. Gong M. Liu L. Zheng Y. Fan Involvement of large conductance Ca(2+)-activated K (+) channel in laminar shear stress-induced inhibition of vascular smooth muscle cell proliferation Pflugers Arch. 2013 465 221 232 10.1007/s00424-012-1182-z
86. S. Y. Ng C. H. Chin Y. T. Lau J. Luo C. K. Wong Z. X. Bian S. Y. Tsang Role of voltage-gated potassium channels in the fate determination of embryonic stem cells J. Cell. Physiol. 2010 224 165 177 10.1002/jcp.22113
87. V. Hinard D. Belin S. Konig C. R. Bader L. Bernheim Initiation of human myoblast differentiation via dephosphorylation of Kir2.1 K + channels at tyrosine 242 Development 2008 135 859 867 10.1242/dev.011387
88. C. M. Root N. A. Velazquez-Ulloa G. C. Monsalve E. Minakova N. C. Spitzer Embryonically expressed GABA and glutamate drive electrical activity regulating neurotransmitter specification J. Neurosci. 2008 28 4777 4784 10.1523/jneurosci.4873-07.2008
89. T. Yasuda D. J. Adams Physiological roles of ion channels in adult neural stem cells and their progeny J. Neurochem. 2010 114 946 959 10.1111/j.1471-4159.2010.06822.x
90. C. Lange S. Prenninger P. Knuckles V. Taylor M. Levin F. Calegari The H(+) vacuolar ATPase maintains neural stem cells in the developing mouse cortex Stem Cells Dev. 2011 20 843 850 10.1089/scd.2010.0484
91. S. Liebau M. Tischendorf D. Ansorge L. Linta M. Stockmann C. Weidgang M. Iacovino T. Boeckers G. von Wichert M. Kyba A. Kleger An inducible expression system of the calcium-activated potassium channel 4 to study the differential impact on embryonic stem cells Stem Cells Int. 2011 2011 456815 10.4061/2011/456815
92. B. Chernet M. Levin Bioelectric signaling in cancer Journal of Experimental and Clinical Oncology 2013
93. S. Hernandez-Diaz M. Levin Alteration of bioelectrically-controlled processes in the embryo: a teratogenic mechanism for anticonvulsants Reprod. Toxicol. 2014 47 111 114 10.1016/j.reprotox.2014.04.008
94. E. A. Bates A potential molecular target for morphological defects of fetal alcohol syndrome: Kir2.1 Curr. Opin. Genet. Dev. 2013 23 324 329 10.1016/j.gde.2013.05.001
95. G. R. Dahal J. Rawson B. Gassaway B. Kwok Y. Tong L. J. Ptacek E. Bates An inwardly rectifying K + channel is required for patterning Development 2012 139 3653 3664 10.1242/dev.078592
96. L. N. Vandenberg R. D. Morrie D. S. Adams V-ATPase-dependent ectodermal voltage and pH regionalization are required for craniofacial morphogenesis Dev. Dyn. 2011 240 1889 1904 10.1002/dvdy.22685
97. M. Levin T. Thorlin K. R. Robinson T. Nogi M. Mercola Asymmetries in H + /K + -ATPase and cell membrane potentials comprise a very early step in left-right patterning Cell 2002 111 77 89
98. W. S. Beane J. Morokuma J. M. Lemire M. Levin Bioelectric signaling regulates head and organ size during planarian regeneration Development 2013 140 313 322 10.1242/dev.086900
99. S. Perathoner J. M. Daane U. Henrion G. Seebohm C. W. Higdon S. L. Johnson C. Nusslein-Volhard M. P. Harris Bioelectric signaling regulates size in zebrafish fins PLoS Genet. 2014 10 e1004080 10.1371/journal.pgen.1004080
100. V. P. Pai J. M. Lemire Y. Chen G. Lin M. Levin Local and long-range endogenous resting potential gradients antagonistically regulate apoptosis and proliferation in the embryonic CNS. Int. J. Dev. Biol. 2015 10.1387/ijdb.150197ml
101. J. Monteiro R. Aires J. D. Becker A. Jacinto A. C. Certal J. Rodriguez-Leon V-ATPase Proton Pumping Activity Is Required for Adult Zebrafish Appendage Regeneration PLoS One 2014 9 e92594 10.1371/journal.pone.0092594
102. R. J. Nuckels A. Ng T. Darland J. M. Gross The vacuolar-ATPase complex regulates retinoblast proliferation and survival, photoreceptor morphogenesis, and pigmentation in the zebrafish eye Invest. Ophthalmol. Visual Sci. 2009 50 893 905
103. S. Bovetti T. Fellin Optical dissection of brain circuits with patterned illumination through the phase modulation of light J. Neurosci. Methods 2015 241 66 77 10.1016/j.jneumeth.2014.12.002
104. M. Hashimoto A. Hata T. Miyata H. Hirase Programmable wireless light-emitting diode stimulator for chronic stimulation of optogenetic molecules in freely moving mice Neurophotonics 2014 1 011002 10.1117/1.NPh.1.1.011002
105. S. Seeger-Armbruster C. Bosch-Bouju S. T. Little R. A. Smither S. M. Hughes B. I. Hyland L. C. Parr-Brownlie Patterned, but not tonic, optogenetic stimulation in motor thalamus improves reaching in acute drug-induced Parkinsonian rats J. Neurosci. 2015 35 1211 1216 10.1523/jneurosci.3277-14.2015
106. E. S. Gil B. Panilaitis E. Bellas D. L. Kaplan Functionalized silk biomaterials for wound healing Adv. Healthcare Mater. 2013 2 206 217 10.1002/adhm.201200192
107. A. S. Tseng W. S. Beane J. M. Lemire A. Masi M. Levin Induction of vertebrate regeneration by a transient sodium current J. Neurosci. 2010 30 13192 13200 10.1523/jneurosci.3315-10.2010
108. G. Buzsaki Neural syntax: cell assemblies, synapsembles, and readers Neuron 2010 68 362 385 10.1016/j.neuron.2010.09.023
109. O. Sporns, Networks of the brain, MIT Press, Cambridge, Mass., 2011, pp. xi, 412, 8 of plates
110. J. Gallaher M. Bier J. S. van Heukelom First order phase transition and hysteresis in a cell's maintenance of the membrane potential-An essential role for the inward potassium rectifiers BioSystems 2010 101 149 155 10.1016/j.biosystems.2010.05.007
111. E. Salo J. F. Abril T. Adell F. Cebria K. Eckelt E. Fernandez-Taboada M. Handberg-Thorsager M. Iglesias M. D. Molina G. Rodriguez-Esteban Planarian regeneration: achievements and future directions after 20 years of research Int. J. Dev. Biol. 2009 53 1317 1327 10.1387/ijdb.072414es
112. E. Marder Electrical synapses: rectification demystified Curr. Biol. 2009 19 R34 R35 10.1016/j.cub.2008.11.008
113. E. Scemes S. O. Suadicani G. Dahl D. C. Spray Connexin and pannexin mediated cell-cell communication Neuron Glia Biol. 2007 3 199 208
114. M. J. Blythe D. Kao S. Malla J. Rowsell R. Wilson D. Evans J. Jowett A. Hall V. Lemay S. Lam A. A. Aboobaker A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology PLoS One 2010 5 e15617 10.1371/journal.pone.0015617
115. D. Lobo T. J. Malone M. Levin Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis Biol. Open 2013 2 156 169 10.1242/bio.20123400
116. R. Law M. Levin Bioelectric memory: modeling resting potential bistability in amphibian embryos and mammalian cells Theor. Biol. Med. Modell. 2015 12 22
117. J. Cervera J. A. Manzanares S. Mafe Electrical Coupling in Ensembles of Nonexcitable Cells: Modeling the Spatial Map of Single Cell Potentials J. Phys. Chem. B 2015 119 2968 2978
118. J. Cervera A. Alcaraz S. Mafe Membrane potential bistability in nonexcitable cells as described by inward and outward voltage-gated ion channels J. Phys. Chem. B 2014 118 12444 12450 10.1021/jp508304h
119. M. Sehgal C. Song V. L. Ehlers J. R. Moyer Jr. Learning to learn-intrinsic plasticity as a metaplasticity mechanism for memory formation Neurobiol. Learn. Mem. 2013 105 186 199 10.1016/j.nlm.2013.07.008
120. D. E. Rumelhart and J. L. McClelland, University of California San Diego. PDP Research Group, Parallel distributed processing: explorations in the microstructure of cognition, MIT Press, Cambridge, Mass., 1986
121. G. A. Buznikov Y. B. Shmukler Possible role of "prenervous" neurotransmitters in cellular interactions of early embryogenesis: a hypothesis Neurochem. Res. 1981 6 55 68
122. F. Keijzer M. van Duijn P. Lyon What nervous systems do: early evolution, input-output, and the skin brain thesis Adapt Behav. 2013 21 67 85 10.1177/1059712312465330
123. M. Levin G. A. Buznikov J. M. Lauder Of minds and embryos: left-right asymmetry and the serotonergic controls of pre-neural morphogenesis Dev. Neurosci. 2006 28 171 185
124. J. Mustard M. Levin Bioelectrical Mechanisms for Programming Growth and Form: Taming Physiological Networks for Soft Body Robotics Soft Robotics 2014 1 169 191 10.1089/soro.2014.0011
125. S. Walker L. Cisneros P. C. W. Davies Evolutionary Transitions and Top-Down Causation Artificial Life 2012 13 283 290
126. E. R. Scerri Top-down causation regarding the chemistry-physics interface: a sceptical view Interface Focus 2012 2 20 25 10.1098/Rsfs.2011.0061
127. S. Okasha Emergence, hierarchy and top-down causation in evolutionary biology Interface Focus 2012 2 49 54 10.1098/Rsfs.2011.0046
128. J. Butterfield Laws, causation and dynamics at different levels Interface Focus 2012 2 101 114 10.1098/Rsfs.2011.0052
129. A. Juarrero Top-Down Causation and Autonomy in Complex Systems Underst Complex Syst 2009 83 102 10.1007/978-3-642-03205-9-5
130. G. F. R. Ellis Top-down causation and emergence: some comments on mechanisms Interface Focus 2012 2 126 140 10.1098/Rsfs.2011.0062
131. E. P. Hoel L. Albantakis G. Tononi Quantifying causal emergence shows that macro can beat micro Proc. Natl. Acad. Sci. U. S. A. 2013 110 19790 19795
132. A. Munjal J. M. Philippe E. Munro T. Lecuit A self-organized biomechanical network drives shape changes during tissue morphogenesis Nature 2015 524 351 355 10.1038/nature14603
133. L. V. Beloussov Morphogenesis as a macroscopic self-organizing process BioSystems 2012 109 262 279 10.1016/j.biosystems.2012.05.003
134. L. V. Beloussov Mechanically based generative laws of morphogenesis Phys. Biol. 2008 5 015009 10.1088/1478-3975/5/1/015009
135. S. Ramirez X. Liu P. A. Lin J. Suh M. Pignatelli R. L. Redondo T. J. Ryan S. Tonegawa Creating a false memory in the hippocampus Science 2013 341 387 391 10.1126/science.1239073
136. X. Liu S. Ramirez P. T. Pang C. B. Puryear A. Govindarajan K. Deisseroth S. Tonegawa Nature 2012 484 381 385 10.1038/nature11028
137. A. Iriki M. Tanaka Y. Iwamura Coding of modified body schema during tool use by macaque postcentral neurones NeuroReport 1996 7 2325 2330
138. L. V. Beloussov Morphogenetic fields: Outlining the alternatives and enlarging the context Riv. Biol.-Biol. Forum 2001 94 219 235
139. N. Morozova and M. Shubin, in Pattern Formation in Morphogenesis, ed., V. Capasso, M. Gromov, A. Harel-Bellan, N. Morozova, and, L. L. Pritchard, Springer, Berlin Heidelberg, 2013, vol. 15, pp. 255-282
140. M. Levin Morphogenetic fields in embryogenesis, regeneration, and cancer: non-local control of complex patterning BioSystems 2012 109 243 261 10.1016/j.biosystems.2012.04.005
141. K. Friston The free-energy principle: a unified brain theory? Nat. Rev. Neurosci. 2010 11 127 138 10.1038/nrn2787
142. B. Sengupta M. B. Stemmler K. J. Friston Information and efficiency in the nervous system-a synthesis PLoS Comput. Biol. 2013 9 e1003157 10.1371/journal.pcbi.1003157
143. K. Friston Active inference and free energy Behavioral and brain sciences 2013 36 212 213 10.1017/S0140525X12002142
144. J. Bongard V. Zykov H. Lipson Resilient machines through continuous self-modeling Science 2006 314 1118 1121 10.1126/science.1133687
145. G. von Dassow E. Munro Modularity in animal development and evolution: elements of a conceptual framework for EvoDevo J. Exp. Zool. 1999 285 307 325
146. K. Friston M. Levin B. Sengupta G. Pezzulo Knowing one's place: a free-energy approach to pattern regulation J. R. Soc., Interface 2015 12 10.1098/rsif.2014.1383
147. I. D. Couzin J. Krause R. James G. D. Ruxton N. R. Franks Collective memory and spatial sorting in animal groups J. Theor. Biol. 2002 218 1 11
148. I. Couzin Collective minds Nature 2007 445 715 10.1038/445715a
149. J. E. Mittenthal R. M. Mazo A model for shape generation by strain and cell-cell adhesion in the epithelium of an arthropod leg segment J. Theor. Biol. 1983 100 443 483
150. J. E. Mittenthal The rule of normal neighbors: a hypothesis for morphogenetic pattern regulation Dev. Biol. 1981 88 15 26 0012-1606(81)90215-3
151. J. D. Orth I. Thiele B. O. Palsson What is flux balance analysis? Nat. Biotechnol. 2010 28 245 248 10.1038/nbt.1614
152. E. P. Gianchandani A. K. Chavali J. A. Papin The application of flux balance analysis in systems biology Wiley Interdiscip. Rev.: Syst. Biol. Med. 2010 2 372 382 10.1002/wsbm.60
153. J. M. Lee E. P. Gianchandani J. A. Papin Flux balance analysis in the era of metabolomics Briefings Bioinf. 2006 7 140 150 10.1093/bib/bbl007
154. H. S. Song J. A. Morgan D. Ramkrishna Systematic development of hybrid cybernetic models: application to recombinant yeast co-consuming glucose and xylose Biotechnol. Bioeng. 2009 103 984 1002 10.1002/bit.22332
155. L. Alvarez B. M. Friedrich G. Gompper U. B. Kaupp The computational sperm cell Trends Cell Biol. 2014 24 198 207
156. L. Zhu M. Aono S. J. Kim M. Hara Amoeba-based computing for traveling salesman problem: Long-term correlations between spatially separated individual cells of Physarum polycephalum BioSystems 2013 112 1 10 10.1016/j.biosystems.2013.01.008
157. F. Caudron Y. Barral A super-assembly of Whi3 encodes memory of deceptive encounters by single cells during yeast courtship Cell 2013 155 1244 1257 10.1016/j.cell.2013.10.046
158. M. Gagliano M. Renton M. Depczynski S. Mancuso Experience teaches plants to learn faster and forget slower in environments where it matters Oecologia 2014 175 63 72 10.1007/s00442-013-2873-7
159. S. Sahu S. Ghosh K. Hirata D. Fujita A. Bandyopadhyay Multi-level memory-switching properties of a single brain microtubule Appl. Phys. Lett. 2013 102 123701 10.1063/1.4793995
160. A. G. Volkov H. Carrell T. Adesina V. S. Markin E. Jovanov Plant electrical memory Plant Signaling Behav. 2008 3 490 492
161. C. H. Turner A. G. Robling R. L. Duncan D. B. Burr Do bone cells behave like a neuronal network? Calcif. Tissue Int. 2002 70 435 442
162. G. J. Spencer P. G. Genever BMC Cell Biol. 2003 4 9 10.1186/1471-2121-4-9
163. M. Zoghi Cardiac memory: do the heart and the brain remember the same? J. Interv. Card. Electrophysiol. 2004 11 177 182
164. S. V. Chakravarthy J. Ghosh On Hebbian-like adaptation in heart muscle: a proposal for 'cardiac memory' Biol. Cybern. 1997 76 207 215
165. K. Deisseroth R. C. Malenka GABA excitation in the adult brain: a mechanism for excitation-neurogenesis coupling Neuron 2005 47 775 777 10.1016/j.neuron.2005.08.029
166. S. Malmersjo P. Rebellato E. Smedler H. Planert S. Kanatani I. Liste E. Nanou H. Sunner S. Abdelhady S. Zhang M. Andang A. El Manira G. Silberberg E. Arenas P. Uhlen Neural progenitors organize in small-world networks to promote cell proliferation Proc. Natl. Acad. Sci. U. S. A. 2013 110 E1524 E1532 10.1073/pnas.1220179110
167. M. R. Popovic N. Kapadia V. Zivanovic J. C. Furlan B. C. Craven C. McGillivray Functional electrical stimulation therapy of voluntary grasping versus only conventional rehabilitation for patients with subacute incomplete tetraplegia: a randomized clinical trial Neurorehabil. Neural. Repair. 2011 25 433 442 10.1177/1545968310392924
168. G. B. Wislocki M. Singer The occurrence and function of nerves in the growing antlers of deer J. Comp. Neurol. 1946 85 1 19
169. A. Kumar J. P. Brockes Nerve dependence in tissue, organ, and appendage regeneration Trends Neurosci. 2012 35 691 969 10.1016/j.tins.2012.08.003
170. C. L. Yntema Regeneration in sparsely innervated and aneurogenic forelimbs of Amblystoma larvae J. Exp. Zool. 1959 140 101 123
171. V. Kiortsis and M. Moraitou, in Regeneration in Animals and Related Problems, ed., V. Kiortsis, and, H. A. L. Trampusch, Amsterdam, 1965, pp. 250-261
172. J. P. Mondia M. Levin F. G. Omenetto R. D. Orendorff M. R. Branch D. S. Adams Long-distance signals are required for morphogenesis of the regenerating Xenopus tadpole tail, as shown by femtosecond-laser ablation PLoS One 2011 6 e24953 10.1371/journal.pone.0024953
173. A. Boettiger B. Ermentrout G. Oster The neural origins of shell structure and pattern in aquatic mollusks Proc. Natl. Acad. Sci. U. S. A. 2009 106 6837 6842 10.1073/pnas.0810311106
174. S. Grossberg, in Progress in Theoretical Biology, ed., R. Rosen, and, F. Snell, 1978, vol. 5
175. A. Gierer H. Meinhardt A theory of biological pattern formation Kybernetik 1972 12 30 39
176. H. K. Hartline H. G. Wagner F. Ratliff Inhibition in the eye of Limulus J. Gen. Physiol. 1956 39 651 673
177. M. Kragl D. Knapp E. Nacu S. Khattak M. Maden H. H. Epperlein E. M. Tanaka Cells keep a memory of their tissue origin during axolotl limb regeneration Nature 2009 460 60 65 10.1038/nature08152
178. L. V. Beloussov On the active memory in developing systems Riv. Biol.-Biol. Forum 1997 90 31 46
179. P. Goel A. Mehta Learning theories reveal loss of pancreatic electrical connectivity in diabetes as an adaptive response PLoS One 2013 8 e70366 10.1371/journal.pone.0070366
180. R. M. Cooper N. S. Wingreen E. C. Cox An excitable cortex and memory model successfully predicts new pseudopod dynamics PLoS One 2012 7 e33528 10.1371/journal.pone.0033528
181. H. Ling S. Samarasinghe D. Kulasiri Novel recurrent neural network for modelling biological networks: oscillatory p53 interaction dynamics BioSystems 2013 114 191 205 10.1016/j.biosystems.2013.08.004
182. R. A. Watson, C. L. Buckley, R. Mills, A. Davies, Artificial Life Conference XII, Odense, Denmark, 2010, pp. 194-201
183. Y. P. Gunji R. Ono Sociality of an agent during morphogenetic canalization: asynchronous updating with potential resonance BioSystems 2012 109 420 429 10.1016/j.biosystems.2012.05.005
184. A. D. Economou A. Ohazama T. Porntaveetus P. T. Sharpe S. Kondo M. A. Basson A. Gritli-Linde M. T. Cobourne J. B. Green Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate Nat. Genet. 2012 44 348 351 10.1038/ng.1090
185. A. Adamatzky B. D. L. Costello T. Shirakawa Universal Computation with Limited Resources: Belousov-Zhabotinsky and Physarum Computers Int. J. Bifurcation Chaos Appl. Sci. Eng. 2008 18 2373 2389
186. S. Scarle. Microsoft, 2008
187. A. Schumann A. Adamatzky Toward semantical model of reaction-diffusion computing Kybernetes 2009 38 1518 1531 10.1108/03684920910991504
188. V. Paquette J. Levesque B. Mensour J. M. Leroux G. Beaudoin P. Bourgouin M. Beauregard "Change the mind and you change the brain": effects of cognitive-behavioral therapy on the neural correlates of spider phobia NeuroImage 2003 18 401 409
189. E. Luders A. W. Toga N. Lepore C. Gaser The underlying anatomical correlates of long-term meditation: larger hippocampal and frontal volumes of gray matter NeuroImage 2009 45 672 678
190. S. E. Webb A. L. Miller Calcium signalling during embryonic development Nat. Rev. Mol. Cell Biol. 2003 4 539 551
191. J. X. Shen D. Qin H. Wang C. Wu F. D. Shi J. Wu Roles of Nicotinic Acetylcholine Receptors in Stem Cell Survival/Apoptosis, Proliferation and Differentiation Curr. Mol. Med. 2013 13 1455 1464
192. D. Villar D. J. Schaeffer Morphogenetic action of neurotransmitters on regenerating planarians-a review Biomed. Environ. Sci. 1993 6 327 347
193. V. Sukhov V. Nerush L. Orlova V. Vodeneev Simulation of action potential propagation in plants J. Theor. Biol. 2011 291C 47 55 10.1016/j.jtbi.2011.09.019
194. G. G. Turrigiano E. Marder L. F. Abbott Cellular short-term memory from a slow potassium conductance J. Neurophysiol. 1996 75 963 966
195. E. Marder L. F. Abbott G. G. Turrigiano Z. Liu J. Golowasch Memory from the dynamics of intrinsic membrane currents Proc. Natl. Acad. Sci. U. S. A. 1996 93 13481 13486
196. G. Buznikov Y. Shmukler J. Lauder From oocyte to neuron: do neurotransmitters function in the same way throughout development? Cell. Mol. Neurobiol. 1996 16 537 559
197. G. Fankhauser Maintenance of normal structure in heteroploid salamander larvae, through compensation of changes in cell size by adjustment of cell number and cell shape J. Exp. Zool. 1945 100 445 455 10.1002/jez.1401000310
198. Y. Kitabatake K. A. Sailor G. L. Ming H. Song Adult neurogenesis and hippocampal memory function: new cells, more plasticity, new memories? Neurosurg. Clin. N. Am. 2007 18 105 113 10.1016/j.nec.2006.10.008
199. J. P. Lerch A. P. Yiu A. Martinez-Canabal T. Pekar V. D. Bohbot P. W. Frankland R. M. Henkelman S. A. Josselyn J. G. Sled NeuroImage 2011 54 2086 2095 10.1016/j.neuroimage.2010.09.086
200. S. Nishimoto A. T. Vu T. Naselaris Y. Benjamini B. Yu J. L. Gallant Curr. Biol. 2011 21 1641 1646 10.1016/j.cub.2011.08.031
201. A. G. Huth S. Nishimoto A. T. Vu J. L. Gallant Neuron 2012 76 1210 1224 10.1016/j.neuron.2012.10.014
202. G. Schlosser and G. P. Wagner, Modularity in development and evolution, University of Chicago Press, Chicago, 2004, p x, 600 p
203. D. Maisto F. Donnarumma G. Pezzulo J. R. Soc., Interface 2015 12 20141335 10.1098/rsif.2014.1335
204. J. J. Wade L. J. McDaid J. Harkin V. Crunelli J. A. Kelso Bidirectional coupling between astrocytes and neurons mediates learning and dynamic coordination in the brain: a multiple modeling approach PLoS One 2011 6 e29445 10.1371/journal.pone.0029445
205. R. Moraga-Amaro J. M. Jerez-Baraona F. Simon J. Stehberg Role of Astrocytes in memory and psychiatric disorders J. Physiol. 2014 108 240 251
206. H. Y. Chang J. T. Chi S. Dudoit C. Bondre M. van de Rijn D. Botstein P. O. Brown Proc. Natl. Acad. Sci. U. S. A. 2002 99 12877 12882 10.1073/pnas.162488599
207. J. L. Rinn C. Bondre H. B. Gladstone P. O. Brown H. Y. Chang Anatomic demarcation by positional variation in fibroblast gene expression programs PLoS Genet. 2006 2 e119 10.1371/journal.pgen.0020119
208. K. C. Wang J. A. Helms H. Y. Chang Regeneration, repair and remembering identity: the three Rs of Hox gene expression Trends Cell Biol. 2009 19 268 275 10.1016/j.tcb.2009.03.007
209. S. Kawamoto C. Yoshida-Noro S. Tochinai Bipolar head regeneration induced by artificial amputation in Enchytraeus japonensis (Annelida, Oligochaeta) J. Exp. Zool., Part A 2005 303 615 627
210. S. R. Williams S. R. Christensen G. J. Stuart M. Hausser Membrane potential bistability is controlled by the hyperpolarization-activated current I(H) in rat cerebellar Purkinje neurons in vitro J. Physiol. 2002 539 469 483
211. Z. C. Chao D. J. Bakkum S. M. Potter Shaping embodied neural networks for adaptive goal-directed behavior PLoS Comput. Biol. 2008 4 e1000042 10.1371/journal.pcbi.1000042
212. J. M. Slack A serial threshold theory of regeneration J. Theor. Biol. 1980 82 105 140
213. T. B. DeMarse K. P. Dockendorf Adaptive flight control with living neuronal networks on microelectrode arrays Ieee Ijcnn 2005 1548 1551
214. A. Adamatzky R. Alonso-Sanz Rebuilding Iberian motorways with slime mould BioSystems 2011 105 89 100 10.1016/j.biosystems.2011.03.007
215. D. J. Blackiston E. Silva Casey M. R. Weiss Retention of memory through metamorphosis: can a moth remember what it learned as a caterpillar? PLoS One 2008 3 e1736 10.1371/journal.pone.0001736
216. T. Shomrat M. Levin An automated training paradigm reveals long-term memory in planarians and its persistence through head regeneration J. Exp. Biol. 2013 216 3799 3810 10.1242/jeb.087809
217. K. Friston F. Rigoli D. Ognibene C. Mathys T. FitzGerald G. Pezzulo Active inference and epistemic value Cogn. Neurosci. 2015 6 187 214
218. K. Friston B. Sengupta G. Auletta Cognitive Dynamics: From Attractors to Active Inference Proc. IEEE 2014 102 427 445 10.1109/Jproc.2014.2306251
219. K. Friston P. Schwartenbeck T. Fitzgerald M. Moutoussis T. Behrens R. J. Dolan The anatomy of choice: active inference and agency Front. Hum. Neurosci. 2013 7 598 10.3389/fnhum.2013.00598
220. C. A. Yates R. Erban C. Escudero I. D. Couzin J. Buhl I. G. Kevrekidis P. K. Maini D. J. Sumpter Inherent noise can facilitate coherence in collective swarm motion Proc. Natl. Acad. Sci. U. S. A. 2009 106 5464 5469 10.1073/pnas.0811195106
221. E. Ben-Jacob Learning from bacteria about natural information processing Ann. N. Y. Acad. Sci. 2009 1178 78 90 10.1111/j.1749-6632.2009.05022.x
222. G. Pezzulo C. Castelfranchi Thinking as the control of imagination: a conceptual framework for goal-directed systems Psychol. Res. 2009 73 559 577 10.1007/S00426-009-0237-Z
223. P. Cisek Beyond the computer metaphor: Behavior as interaction Journal of Consciousness Studies 1999 6 125 142
224. K. J. Friston J. Daunizeau J. Kilner S. J. Kiebel Action and behavior: a free-energy formulation Biol. Cybern. 2010 102 227 260 10.1007/s00422-010-0364-z
225. M. Desmurget S. Grafton Forward modeling allows feedback control for fast reaching movements Trends Cognit. Sci. 2000 4 423 431
226. G. Pezzulo M. A. van der Meer C. S. Lansink C. M. A. Pennartz Internally generated sequences in learning and executing goal-directed behavior Trends Cognit. Sci. 2014 18 647 657
227. P. F. M. J. Verschure C. M. A. Pennartz G. Pezzulo The why, what, where, when and how of goal-directed choice: neuronal and computational principles Philos. Trans. R. Soc., B 2014 369 20130483
228. G. A. Miller, Plans and the structure of behavior, Holt, New York, 1960, p. 226
229. W. T. Powers, Behavior: the control of perception, Aldine Pub. Co., Chicago, 1973, pp. xi, 296
230. J. Neumann, in Modern Systems Research for the Behavioral Scientist, ed., W. Buckley, 1951, pp. 97-108
231. R. Shadmehr M. A. Smith J. W. Krakauer Error correction, sensory prediction, and adaptation in motor control Annu. Rev. Neurosci. 2010 33 89 108 10.1146/annurev-neuro-060909-153135
232. R. C. Conant W. R. Ashby Every good regulator of a system must be a model of that system Intl. J. Systems Science 1970 89 97
233. D. M. Wolpert and Z. Ghahramani, Computational Motor Control. Cognitive Neurosciences Iii, 3rd edn, 2004, pp. 485-493
234. M. Jeannerod Neural simulation of action: A unifying mechanism for motor cognition NeuroImage 2001 14 S103 S109
235. G. Pezzulo C. Castelfranchi Thinking as the Control of Imagination: a Conceptual Framework for Goal-Directed Systems Psychol. Res. 2009 73 559 577
236. E. Todorov Efficient computation of optimal actions Proc. Natl. Acad. Sci. U. S. A. 2009 106 11478 11483
237. M. Botvinick M. Toussaint Planning as inference Trends Cognit. Sci. 2012 16 485 488
238. P. A. Ortega D. A. Braun Thermodynamics as a theory of decision-making with information-processing costs Proc. R. Soc. A 2013 469
239. H. J. Kappen V. Gomez M. Opper Optimal control as a graphical model inference problem Machine Learning 2012 87 159 182 10.1007/S10994-012-5278-7
240. K. Friston S. Samothrakis R. Montague Active inference and agency: optimal control without cost functions Biol. Cybern. 2012 106 523 541 10.1007/s00422-012-0512-8
241. D. J. Blackiston M. Levin Ectopic eyes outside the head in Xenopus tadpoles provide sensory data for light-mediated learning J. Exp. Biol. 2013 216 1031 1040 10.1242/jeb.074963
242. G. E. Hinton Learning multiple layers of representation Trends Cognit. Sci. 2007 11 428 434 10.1016/J.Tics.2007.09.004
243. J. Dean, G. Corrado, R. Monga, K. Chen, M. Devin, M. Mao, M. Ranzato, A. E. Senior, P. Tucker, K. Yang, Q. V. Le and A. Y. Ng, Advances in Neural Information Processing Systems, 2012, vol. 25, pp. 1232-1240
244. H. V. Helmholtz and J. P. C. Southall, Helmholtz's treatise on physiological optics, The Optical Society of America, Rochester, N.Y., 1924
245. R. P. Rao D. H. Ballard Predictive coding in the visual cortex: a functional interpretation of some extra-classical receptive-field effects Nat. Neurosci. 1999 2 79 87 10.1038/4580
246. A. Rosenblueth N. Wiener J. Bigelow Behavior, purpose, and teleology Philos. Sci. 1943 10 18 24
247. I. Stoianov A. Genovesio G. Pezzulo Prefrontal Goal Codes Emerge as Latent States in Probabilistic Value Learning J. Cogn. Neurosci. 2015 1 18
248. G. Pezzulo F. Rigoli K. Friston Active Inference, homeostatic regulation and adaptive behavioural control Prog. Neurobiol. 2015 10.1016/j.pneurobio.2015.09.001
249. K. Friston Life as we know it J. R. Soc., Interface 2013 10 20130475
250. S. Wolfram, A new kind of science, Wolfram Media, Champaign, IL, 2002, pp. xiv, 1197
251. J. J. Hopfield Neural networks and physical systems with emergent collective computational abilities Proc. Natl. Acad. Sci. U. S. A. 1982 79 2554 2558
252. P. C. Davies L. Demetrius J. A. Tuszynski Cancer as a dynamical phase transition Theor. Biol. Med. Modell. 2011 8 30 10.1186/1742-4682-8-30
253. S. Huang I. Ernberg S. Kauffman Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective Semin. Cell Dev. Biol. 2009 20 869 876 10.1016/j.semcdb.2009.07.003
254. R. V. Sole J. Macia Expanding the landscape of biological computation with synthetic multicellular consortia Nat. Comput. 2013 12 485 497 10.1007/S11047-013-9380-Y
255. K. J. Friston T. Shiner T. FitzGerald J. M. Galea R. Adams H. Brown R. J. Dolan R. Moran K. E. Stephan S. Bestmann Dopamine, affordance and active inference PLoS Comput. Biol. 2012 8 e1002327 10.1371/journal.pcbi.1002327
256. J. A. Edlund N. Chaumont A. Hintze C. Koch G. Tononi C. Adami Integrated information increases with fitness in the evolution of animats PLoS Comput. Biol. 2011 7 e1002236 10.1371/journal.pcbi.1002236
257. D. Balduzzi G. Tononi Integrated information in discrete dynamical systems: motivation and theoretical framework PLoS Comput. Biol. 2008 4 e1000091 10.1371/journal.pcbi.1000091
258. A. S. Klyubin D. Polani C. L. Nehaniv Empowerment: a universal agent-centric measure of control Ieee C Evol. Computat. 2005 128 135
259. G. Martius, J. M. Herrmann and R. Der, in Advances in Artificial Life, ed., F. Almeida e Costa, L. Rocha, E. Costa, I. Harvey, and, A. N. Coutinho, Springer, Berlin, Heidelberg, 2007, vol. 4648, pp. 766-775
260. G. Auletta Teleonomy: The Feedback Circuit involving Information and Thermodynamic Processes J. Mod. Phys. 2011 2 136 145 10.4236/jmp.2011.23021
261. G. Tononi Consciousness as integrated information: a provisional manifesto Biol. Bull. 2008 215 216 242
262. E. Bullmore O. Sporns Complex brain networks: graph theoretical analysis of structural and functional systems Nat. Rev. Neurosci. 2009 10 186 198 10.1038/nrn2575
263. A. B. Bubenik R. Pavlansky Trophic responses to trauma in growing antlers J. Exp. Zool. 1965 159 289 302
264. K. D. Birnbaum A. S. Alvarado Slicing across kingdoms: regeneration in plants and animals Cell 2008 132 697 710
265. G. Pezzulo C. Castelfranchi The symbol detachment problem Cogn. Process. 2007 8 115 131 10.1007/s10339-007-0164-0