Papers
“Collective Computation in Animal Fission-Fusion Dynamics.” Gabriel Ramos-Fernandez, Sandra E. Smith Aguilar, David C Krakauer, Jessica D Flack, Front. Robot. AI, 21 July 2020 Volume 7, pages 1-16, (2020)
tags: computation; collective; pattern formation; memory
”The information theory of individuality.” DC Krakauer, N Bertschinger, E Olbrich, JC Flack & N Ay, Theory in Biosciences volume 139, pages 209–223 (2020)
tags: individuality; information; life; modularity; adaptation
”A scaling theory of armed conflict avalanches.” ED Lee, BC Daniels, CR Myers, DC Krakauer, JC Flack. arXiv preprint arXiv: 2004.14311 2020
tags: conflict; warfare; collective
”Emergent regularities and scaling in armed conflict data.” ED Lee, BC Daniels, CR Myers, DC Krakauer, JC Flack. arXiv preprint arXiv:1903.0776 1 2019
tags: conflict; warfare; collective; scaling
”Coarse-graining armed conflict.” E Lee, B Daniels, V Elser, DC Krakauer, J Flack. APS Meeting Abstracts 2019
tags: conflict; warfare; collective; scaling
”The cultural evolution of national constitutions.” DN Rockmore, C Fang, NJ Foti, T Ginsburg, DC Krakauer. Journal of the Association for Information Science and Technology 69, 3--8 (2018)
tags: cultural evolution; regulation; law
”Conflicts of interest improve collective computation of adaptive social structures.” ER Brush, DC Krakauer, JC Flack. Science Advances 4 (1), e1603311 5 (2018)
tags: conflict; warfare; collective; scaling; computation
”Collective memory in primate conflict implied by temporal scaling collapse.”
ED Lee, BC Daniels, DC Krakauer, JC Flack
Journal of The Royal Society Interface 14 (134), 20170223 3 2017
tags: conflict; warfare; collective; scaling; memory
”Dual coding theory explains biphasic collective computation in neural decision-making.”
BC Daniels, JC Flack, DC Krakauer
Frontiers in Neuroscience 11, 313 12 2017
tags: computation; neuroscience; neural computation; information; collective
”Control of finite critical behaviour in a small-scale social system.”
BC Daniels, DC Krakauer, JC Flack
Nature Communications 8 (1), 1-8 34 2017
tags: criticality; collective; cooperation; control; conflict
”Design specifications for cellular regulation.”
DC Krakauer, L Müller, SJ Prohaska, PF Stadler
Theory in Biosciences 135 (4), 231-240 2 2016
tags: regulation; cellular; cell; evolution
”Quantifying collectivity.”
BC Daniels, CJ Ellison, DC Krakauer, JC Flack
Current Opinion in Neurobiology 37, 106-113 23 2016
tags: collectivity; collective; information
”The dynamics of neuronal redundancy in decision making.”
B Daniels, J Flack, DC Krakauer
APS Meeting Abstracts 2016
tags: computation; neuroscience; neural computation; information; collective
”Capturing collective conflict dynamics with sparse social circuits.”
E Lee, B Daniels, J Flack, DC Krakauer
arXiv preprint arXiv:1406.7720 2014
tags: criticality; conflict; collective
”The Computational Systems of the World.”
DC Krakauer
BioScience 64 (4), 351-354 1 2014
tags: computation; intelligence; algorithm
”The inferential evolution of biological complexity: forgetting nature by learning nurture.”
DC Krakauer
Complexity and the Arrow of Time; CH, Davies, PCW, Ruse, M., eds …
42013
tags: evolution; complexity; memory; cryptographic; learning
”A family of algorithms for computing consensus about node state from network data.”
ER Brush, DC Krakauer, JC Flack
PLoS Computational Biology 9 (7)
272013
tags: algorithms; network; coordination; consensus
”Timescales, symmetry, and uncertainty reduction in the origins of hierarchy in biological systems.”
JC Flack, D Erwin, T Elliot, DC Krakauer
Evolution Cooperation and Complexity, 45-74
302013
tags: cooperation; time; symmetry; consensus
”Dynamics and processing in finite self-similar networks.”
S DeDeo, DC Krakauer
Journal of the Royal Society Interface 9 (74), 2131-2144
252012
tags: dynamics; criticality; networks
”Sparse code of conflict in a primate society.”
BC Daniels, DC Krakauer, JC Flack
Proceedings of the National Academy of Sciences 109 (35), 14259-14264
242012
tags: conflict; sparsity; compression; computation
”Quantitative patterns of stylistic influence in the evolution of literature.”
JM Hughes, NJ Foti, DC Krakauer, DN Rockmore
Proceedings of the National Academy of Sciences 109 (20), 7682-7686
1092012
tags: cultural evolution; topic models; complexity; coarse-graining; history
”Robustness in biological and social systems.”
JC Flack, P Hammerstein, DC Krakauer
Evolution and the Mechanisms of Decision-Making, 129-151
82012
tags: robustness; evolution; memory; niche construction
”Timescales, symmetry, and uncertainty reduction in the origins of hierarchy in biological systems.”
J Flack, D Erwin, T Elliot, DC Krakauer Cooperation and Its Evolution 32012 MIT Press 2013
tags: symmetry; timescales; uncertainty; information
”Nonequilibrium phase transitions in biomolecular signal transduction.”
E Smith, S Krishnamurthy, W Fontana, DC Krakauer
Physical Review E 84 (5), 051917
142011
tags: logic; molecule; phase-transition; criticality; cell
”Challenges for complexity measures: A perspective from social dynamics and collective social computation.”
JC Flack, DC Krakauer
Chaos: An Interdisciplinary Journal of Nonlinear Science 21 (3), 037108 362011
tags: computation; complexity; collective
”Darwinian demons, evolutionary complexity, and information maximization.”
DC Krakauer
Chaos: An Interdisciplinary Journal of Nonlinear Science 21 (3), 037110 432011
tags: complexity; evolution; information; coarse-graining; compression; niche construction; emergence
”Evidence of strategic periodicities in collective conflict dynamics.”
S DeDeo, DC Krakauer, J Flack
Journal of The Royal Society Interface 8 (62), 1260-1273
262011
tags: timescales; time; conflict; warfare; collective
”The challenges and scope of theoretical biology.”
DC Krakauer, JP Collins, D Erwin, JC Flack, W Fontana, MD Laubichler, ...
Journal of Theoretical Biology 276 (1), 269-276
602011
tags: theory; math; models; parsimony; evolution; compression; time; emergent
”Laws of cooperation.”
DC Krakauer
Science 332 (6029), 538-539
22011
tags: cooperation; games; evolution
”The Star Gazer and the Flesh Eater: Elements of a Theory of Metahistory.”
DC Krakauer
Cliodynamics, 2 (1)
2011
tags: history; theory; models; parsimony; evolution; dynamics
”The immuno-dynamics of conflict intervention in social systems.”
DC Krakauer, K Page, J Flack
PloS One 6 (8)
142011
tags: conflict; policing; collective; regulation
”Better living through physics.”
DC Krakauer, JC Flack
Nature 467 (7316), 661-661
182010
tags: cooperation; selection; models
”Innovation in gene regulation: the case of chromatin computation.”
SJ Prohaska, PF Stadler, DC Krakauer
Journal of Theoretical Biology 265 (1), 27-44
482010
tags: innovation; regulation; computation; evolution
”Probabilistic design principles for robust multimodal communication networks.”
DC Krakauer, JC Flack, N Ay
Modelling Perception with Artificial Neural Networks, 255-268
12010
tags: robust; emergent; information
”Selfish Games.”
DC Krakauer
Science 328 (5981), 977-978
2010
tags: cooperation; parsimony; modeling; games
”Intelligent data analysis of intelligent systems.”
DC Krakauer, JC Flack, S Dedeo, D Farmer, D Rockmore
International Symposium on Intelligent Data Analysis, 8-17
122010
tags: intelligence; data; compression; dynamics; memory; theory
”Inductive game theory and the dynamics of animal conflict.”
S DeDeo, DC Krakauer, JC Flack
PLoS Computational Biology 6 (5)
542010
tags: game; intelligence; dynamics; parsimony; theory; coarse-graining; information; timescales; cooperation; networks;
”Selection controversies in and out of equilibrium.”
DC Krakauer, JC Flack
Nature 467, P661
2010
tags: selection; cooperation; games; parsimony; coarse-graining; theory
”Fragmentation within matrilineal pedigrees is associated with fragmentation in grooming networks of captive rhesus macaques (macaca mulatta).”
BA Beisner, ME Jackson, A Cameron, JC Flack, DC Krakauer, ...
American Journal of Primatology 71, 54-54 2009
tags: conflict; collective; networks
”Defining genes: a computational framework.”
PF Stadler, SJ Prohaska, CV Forst, DC Krakauer
Theory in Biosciences 128 (3), 165
312009
tags: logic; genes; computation; regulation; modularity; levels of selection
”Évolution, complexité et métahistoricisme.”
DC Krakauer
Nouvelles perspectives en sciences sociales 4 (2), 53-67
22009
tags: history; dynamics; theory
”Evolution and construction of moral systems.”
JC Flack, DC Krakauer
Games, Groups, and the Global Good, 117-141
72009
tags: evolution; niche construction; consensus; cooperation; coordination
”Viral individuality and limitations of the life concept.”
DC Krakauer, PMA Zanotto
Protocells: Bridging Nonliving and Living Matter
242009
tags: viral; microbe; phylogeny; living; life; emergence
”Diversity, dilemmas, and monopolies of niche construction.”
DC Krakauer, KM Page, DH Erwin
The American Naturalist 173 (1), 26-40
862009
tags: niche construction; theory; levels of selection; secrecy; games; individuality
”An end to endless forms: epistasis, phenotype distribution bias, and nonuniform evolution.”
E Borenstein, DC Krakauer
PLoS Computational Biology 4 (10)
562008
tags: development; evolution; pattern formation; emergence
”Developmental autonomy and somatic niche construction promotes robust cell fate decisions.”
AK Bershad, MA Fuentes, DC Krakauer
Journal of Theoretical Biology 254 (2), 408-416
42008
”The evolution of developmental patterning under genetic duplication constraints.”
MA Fuentes, DC Krakauer
Journal of the Royal Society Interface 5 (19), 237-245
32008
tags: development; evolution; pattern formation; emergence; cell
”Complete genome viral phylogenies suggests the concerted evolution of regulatory cores and accessory satellites.”
PM de Andrade Zanotto, DC Krakauer
PLoS One 3 (10)
172008
tags: phylogenies; virus; microbe; experimental evolution; regulation; levels of selection; compression
”A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes.”
F Lillo, DC Krakauer
Biology Direct 2 (1), 22
272007
tags: compression; phylogenies; microbe; selection; sparsity; molecule; individuality
”The stochastic behavior of a molecular switching circuit with feedback.”
S Krishnamurthy, E Smith, DC Krakauer, W Fontana
Biology Direct 2 (1), 13
202007
tags: criticality; phase-transition; individuality; collective; scaling; compression; computation; robustness
”The Universal Darwinism of Disease.”
DC Krakauer
Science 318 (5853), 1070-1070
2007
tags: disease; selection; theory; modeling; evolution
”Geometric robustness theory and biological networks.”
N Ay, DC Krakauer
Theory in Biosciences 125 (2), 93-121
482007
tags: information; robustness; theory; causality; neural network; memory
”Robustness and complexity co-constructed in multimodal signalling networks.”
N Ay, J Flack, DC Krakauer
Philosophical Transactions of the Royal Society B: Biological Sciences 362 …
702007
tags: information; robustness; theory; causality; neural network; memory
”Encoding power in communication networks.”
JC Flack, DC Krakauer
The American Naturalist 168 (3), E87-E102
562006
tags: power; communication; networks; complexity; computation
”The greater than twofold cost of integration for retroviruses.”
DC Krakauer, A Sasaki
Proceedings of the Royal Society B: Biological Sciences 273 (1590), 1159-1163
12006
tags: virus; microbe; levels of selection; emergence; individuality; criticality
”Robustness in biological systems: a provisional taxonomy.”
DC Krakauer
Complex Systems Science in Biomedicine, 183-205
532006
tags: robustness; molecular; theory; modeling; collective dynamics; symmetry; evolution
”Policing stabilizes construction of social niches in primates.”
JC Flack, M Girvan, FBM De Waal, DC Krakauer
Nature 439 (7075), 426-429
5972006
tags: policing; conflict; niche construction; coordination; cooperation; robustness
”Robustness mechanisms in primate societies: a perturbation study.”
JC Flack, DC Krakauer, FBM de Waal
Proceedings of the Royal Society B: Biological Sciences 272 (1568), 1091-1099
1432005
tags: policing; conflict; niche construction; coordination; cooperation; robustness
”Social structure, robustness, and policing cost in a cognitively sophisticated species.”
JC Flack, FBM De Waal, DC Krakauer
The American Naturalist 165 (5), E126-E139
1922005
tags: policing; conflict; niche construction; coordination; cooperation; robustness; intelligence
”Principles and Parameters of Molecular Robustness.”
DC Krakauer, JB Plotkin
Robust Design: A Repertoire of Biological, Ecological, and Engineering Case …
252005
tags: robustness; molecular; cell; levels of selection; games
”What moves prices? An approach based on empirical behavioral models and evolving ecologies of arbitraguers.” J. Doyne Farmer, James Angel, Marcus Daniels, John Geanakoplos, Burton Hollifield, David Krakauer, Blake LeBaron and Fabrizio Lillo. Research Net. Feb. 2005.
tags: dynamics; ecologies; economics; experimental evolution; causality
”Living and nonliving matter-response.”
S Rasmussen, MA Bedau, LH Chen, DW Deamer, DC Krakauer, ...
Science 305 (5680), 41-43
2 2004
tags: living; origin of life; exobiology; theory; emergence; experimental evolution
”Insights into innovation.”
DH Erwin, DC Krakauer
Science 304 (5674), 1117-1119
1032004
tags: evolution; innovation; selection; phylogeny; timescales
”Transitions from nonliving to living matter.”
S Rasmussen, L Chen, D Deamer, DC Krakauer, NH Packard, PF Stadler, ...
Science 303 (5660), 963-965
3242004
tags: living; origin of life; exobiology; theory; emergence; experimental evolution;
”From physics to phenomenology: levels of description and levels of selection.”
DC Krakauer Novartis Foundation symposium, 42-52 4 2002
tags: physics; theory; parsimony; selection; emergence; evolution
”Levels of selection in positive‐strand virus dynamics.”
DC Krakauer, NL Komarova
Journal of Evolutionary Biology 16 (1), 64-73
462003
tags: selection; virus; microbe; evolution; individuality; coordination
”Noisy clues to the origin of life.”
DC Krakauer, A Sasaki
Proceedings of the Royal Society of London. Series B: Biological Sciences …
16 2002
tags: dynamics; levels of selection; origin of life; exobiology; cell; theory
”Module dynamics of the GnRH signal transduction network.”
DC Krakauer, KM Page, S Sealfon
Journal of Theoretical Biology 218 (4), 457-470
40 2002
tags: computation; cell; collective; molecular; memory; module; modularity; network
”Red queen dynamics of protein translation.”
DC Krakauer, VAA Jansen
Journal of Theoretical Biology 218 (1), 97-109 37 2002
tags: dynamics; levels of selection; origin of life; exobiology; cell; theory
”Evolutionary principles of genomic compression.”
DC Krakauer
Comments® on Theoretical Biology 7 (4), 215-236 19 2002
tags: compression; genomic; evolutionary; sparsity; compression; information; compression; regulation
”Redundancy, antiredundancy, and the robustness of genomes.”
DC Krakauer, JB Plotkin
Proceedings of the National Academy of Sciences 99 (3), 1405-1409 263 2002
tags: robustness; microbe; Adaptation; dynamics; phase-transition
”Red queen dynamics and the evolution of translational redundancy and degeneracy.”
DC Krakauer, VAA Jansen, M Nowak
Biological Evolution and Statistical Physics, 37-54 2002
tags: genomes; compression; cooperation; levels of selection; molecular; cell
”Selective imitation for a private sign system.”
DC Krakauer
Journal of Theoretical Biology 213 (2), 145-157 14 2001
tags: language; linguistics; cultural evolution; games; coordination
”Genetic instability and the evolution of angiogenic tumor cell lines.”
D Wodarz, DC Krakauer
Oncology Reports 8 (6), 1195-1201 21 2001
tags: robustness; disease; dynamics
”Genetic redundancy.”
DC Krakauer
Encyplopedia of the Life Sciences 4 2001
tags: robustness; genomes; evolution; timescales; memory
”Evolving cell death in the virus-infected nervous system.”
DC Krakauer
Trends in Neurosciences 23 (12), 611 3 2000
tags: virus; development; neuroscience; cell; dynamics
”Models of experimental evolution: the role of genetic chance and selective necessity.”
LM Wahl, DC Krakauer
Genetics 156 (3), 1437-1448 67 2000
tags: experimental evolution; microbe; adaptation; selection
”Error, population structure and the origin of diverse sign systems.”
NC Grassly, A Von Haeseler, DC Krakauer
Journal of Theoretical Biology 206 (3), 369-378 18 2000
tags: language; linguistics; cultural evolution; games; coordination
”Mapping the parameters of prion-induced neuropathology.”
MPH Stumpf, DC Krakauer
Proceedings of the National Academy of Sciences 97 (19), 10573-10577 25 2000
tags: cell; Prion; disease; dynamics; theory; network
”Defining CTL-induced pathology: implications for HIV.”
D Wodarz, DC Krakauer
Virology 274 (1), 94-104 57 2000
tags: cell; disease; dynamics; robustness; virus
”Stability and evolution of overlapping genes.”
DC Krakauer
Evolution 54 (3), 731-739 136 2000
tags: genes; genomes; compression; robustness; evolution; evolvability
”Mitochondria and the death of oocytes.”
DC Krakauer, A Mira
Nature 403 (6769), 501-501 12 2000
tags: robustness; development; levels of selection; cell; arena selection
”Communications-Fragile Dominion--A Book Review.”
DC Krakauer, MA Nowak
Notices of the American Mathematical Society 47 (5), 564-568 2000
tags: economics; ecologies
”Disruptive sexual selection.”
RJH Payne, DC Krakauer
Trends in Ecology & Evolution 10 (15), 419-420 7 2000
tags: sexual selection; speciation; space
”An error limit for the evolution of language.”
MA Nowak, DC Krakauer, A Dress
Proceedings of the Royal Society of London. Series B: Biological Sciences … 151 1999
tags: information; language; linguistics; symmetry
”Evolutionary preservation of redundant duplicated genes.”
DC Krakauer, MA Nowak
Seminars in Cell & Developmental Biology 10 (5), 555-559 90 1999
tags: robustness; genomes; timescales; individuality; developmental; memory
”The evolutionary language game.”
MA Nowak, JB Plotkin, DC Krakauer
Journal of Theoretical Biology 200 (2), 147-162 227 1999
tags: game; language; linguistics; cultural evolution
”The evolution of language.”
MA Nowak, DC Krakauer
Proceedings of the National Academy of Sciences 96 (14), 8028-8033 616 1999
tags: game; language; linguistics; cultural evolution
”Mitochondria and germ-cell death.”
DC Krakauer, A Mira
Nature 400 (6740), 125-126 173 1999
tags: robustness; development; levels of selection; cell; arena selection
”T–cell induced pathogenesis in HIV: bystander effects and latent infection.”
DC Krakauer, M Nowak
Proceedings of the Royal Society of London. Series B: Biological Sciences …34 1999
tags: disease; memory; development; virus
”The spatial dynamics of prion disease.”
RJH Payne, DC Krakauer
Proceedings of the Royal Society of London. Series B: Biological Sciences …16 1998
tags: space; prion; disease; dynamics
”Spatial scales of desert locust gregarization.”
M Collett, E Despland, SJ Simpson, DC Krakauer
Proceedings of the National Academy of Sciences 95 (22), 13052-13055 128 1998
tags: spatial; collective; Selection; emergence
”Effect of immune activation on the dynamics of human immunodeficiency virus replication and on the distribution of viral quasispecies.”
MA Ostrowski, DC Krakauer, Y Li, SJ Justement, G Learn, LA Ehler, ...
Journal of Virology 72 (10), 7772-7784 94 1998
tags: disease; memory; development; virus
”Prion's progress: patterns and rates of molecular evolution in relation to spongiform disease.”
DC Krakauer, MA Paolo, M Pagel
Journal of Molecular Evolution 47 (2), 133-145 37 1998
tags: space; prion; disease; dynamics; phylogeny
”The paradoxical dynamics of prion disease latency.”
RJH Payne, DC Krakauer
Journal of Theoretical Biology 191 (4), 345-352 12 1998
tags: space; prion; disease; dynamics; timescales
”Prion infection dynamics.”
MA Nowak, DC Krakauer, A Klug, RM May
Integrative Biology: Issues, News, and Reviews: Published in Association …57 1998
tags: space; prion; disease; dynamics; phase-transition; regulation; timescales
”The evolution of virus–induced apoptosis.”
DC Krakauer, RJH Payne
Proceedings of the Royal Society of London. Series B: Biological Sciences … 26 1997
tags: disease; memory; development; virus; cell
”Is the propagation of prion molecules in different hosts an example of lamarckian inheritance?” Reply from M. Pagel and DC Krakauer
M Pagel, DC Krakauer
Trends in Ecology & Evolution 12 (5), 194 2 1997
tags: prion; cultural evolution; timescales; levels of selection; information
”Sexual selection, space, and speciation.”
RJH Payne, DC Krakauer
Evolution 51 (1), 1-9 143 1997
tags: selection; space; species; dynamics; theory
”The evolutionary imperative and the origin of the prion pathogen.”
DC Krakauer
Nutrition 7 (13), 692-694 1 1997
tags: space; prion; disease; dynamics; phase-transition; regulation; timescales
”Selection by somatic signals: the advertisement of phenotypic state through costly intercellular signals.”
DC Krakauer, M Pagel
Philosophical Transactions of the Royal Society of London. Series B …22 1996
tags: selection; space; arena selection; cell; development; molecules; cooperation
”Phylogenesis of prion protein.”
DC Krakauer, M Pagel, TRE Southwood, MA Paola
Nature 380 (6576), 675-675 51 1996
tags: phylogeny; prion; disease
”Prions and the new molecular phenetics.”
M Pagel, DC Krakauer
Trends in Ecology & Evolution 11 (12), 487-488 9 1996
tags: phylogeny; prion; disease
”Searching and learning in a random environment.”
DC Krakauer, MA Rodrı́guez-Gironés
Journal of Theoretical Biology 177 (4), 417-429 50 1995
tags: learning; memory; adaptation; individuality
”An evolutionary perspective on Hebb's reverberatory representations.”
DC Krakauer, AI Houston
Behavioral and Brain Sciences 18 (4), 636-637 1995
tags: learning; memory
”Spatial structure and the evolution of honest cost-free signalling.”
DC Krakauer, M Pagel
Proceedings of the Royal Society of London. Series B: Biological Sciences … 39 1995
tags: space; cooperation; communication; adaptation; information
”Groups confuse predators by exploiting perceptual bottlenecks: a connectionist model of the confusion effect.”
DC Krakauer
Behavioral Ecology and Sociobiology 36 (6), 421-429 189 1995
tags: neural network; adaptation; collective; information
”The evolution of exploitation and honesty in animal communication: a model using artificial neural networks.”
DC Krakauer, RA Johnstone
Philosophical Transactions of the Royal Society of London. Series B … 50 1995
tags: neural network; adaptation; games; coordination; information; space; learning
”Simple connectionist models of spatial memory in bees.”
DC Krakauer
Journal of Theoretical Biology 172 (2), 149-160 13 1995
tags: neural network; adaptation; collective; information; space; learning
”Spatial structure and the evolution of honest cost-free signalling.”
DC Krakauer, M Pagel
Proc. R. Soc. Lond. B 260, 365-372 1995
tags: space; games; coordination; communication; adaptation
”Hummingbirds as net rate maximisers.”
AI Houston, DC Krakauer
Oecologia 94 (1), 135-138
1 1993
tags: ecology; economics; games; adaptation; evolution