Evolution and Tinkering

Evolution at Two Levels in Humans and Chimpanzees: Their macromolecules are so alike that regulatory mutations may account for their biological differences

King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815

From molecular to modular cell biology.

Hartwell, L. H., Hopfield, J. J., Leibler, S., & Murray, A. W. (1999) · Nature · doi:10.1038/35011540 · Cited by 3,632

Ecosystems and the Biosphere as Complex Adaptive Systems

Levin, S. A. (1998) · Ecosystems · doi:10.1007/s100219900037 · Cited by 1,726

Interacting Minds--A Biological Basis

Frith, C. D., & Frith, U. (1999) · Science · doi:10.1126/science.286.5445.1692 · Cited by 1,714

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

Putnam, N. H., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., Salamov, A., Terry, A., Shapiro, H., Lindquist, E., Kapitonov, V. V., et al. (2007) · Science · doi:10.1126/science.1139158 · Cited by 1,555

Enzyme promiscuity: A mechanistic and evolutionary perspective

Tawfik, O. K. A. D. S. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-030409-143718 · Cited by 1,355

Natural language and natural selection

Pinker, S., & Bloom, P. (1990) · Behavioral and Brain Sciences · doi:10.1017/s0140525x00081061 · Cited by 1,330

Neural reuse: A fundamental organizational principle of the brain

Anderson, M. L. (2010) · Behavioral and Brain Sciences · doi:10.1017/s0140525x10000853 · Cited by 1,212

DNA transposons and the evolution of eukaryotic genomes.

Feschotte, C., & Pritham, E. J. (2007) · Annual Review of Genetics · doi:10.1146/annurev.genet.40.110405.090448 · Cited by 1,218

Homology of the eyeless Gene of Drosophila to the Small eye Gene in Mice and Aniridia in Humans

Quiring, R., Walldorf, U., Kloter, U., & Gehring, W. J. (1994) · Science · doi:10.1126/science.7914031 · Cited by 1,100

Genes, evolution, and personality

Bouchard, T. J., & Loehlin, J. C. (2001) · Behavior Genetics · doi:10.1023/a:1012294324713 · Cited by 1,085

A small step for the cell, a giant leap for mankind: a hypothesis of neocortical expansion during evolution

Rakic, P. (1995) · Trends in Neurosciences · doi:10.1016/0166-2236(95)93934-p · Cited by 1,047

Evolution at Two Levels: On Genes and Form

Carroll, S. B. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030245 · Cited by 882

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

Blount, Z. D., Borland, C. Z., & Lenski, R. E. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803151105 · Cited by 840

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

Ule, J., & Blencowe, B. J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.017 · Cited by 780

The evolutionary origin of orphan genes

Tautz, D., & Domazet-Lošo, T. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3053 · Cited by 764

Pax 6: mastering eye morphogenesis and eye evolution

Gehring, W. J., & Ikeo, K. (1999) · Trends in Genetics · doi:10.1016/s0168-9525(99)01776-x · Cited by 758

Proto-genes and de novo gene birth

Carvunis, A.-R., Rolland, T., Wapinski, I., Calderwood, M. A., Yildirim, M. A., Simonis, N., Charloteaux, B., Hidalgo, C. A., Barbette, J., Santhanam, B., et al. (2012) · Nature · doi:10.1038/nature11184 · Cited by 669

Biological networks: the tinkerer as an engineer

Alon, U. (2003) · Science · doi:10.1126/science.1089072 · Cited by 706

Parsing the neural correlates of moral cognition: ALE meta-analysis on morality, theory of mind, and empathy

Bzdok, D., Schilbach, L., Vogeley, K., Schneider, K., Laird, A. R., Langner, R., & Eickhoff, S. B. (2012) · Brain Structure and Function · doi:10.1007/s00429-012-0380-y · Cited by 653

Enzyme promiscuity: evolutionary and mechanistic aspects

Khersonsky, O., Roodveldt, C., & Tawfik, D. S. (2006) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2006.08.011 · Cited by 641

Genomic analysis of a key innovation in an experimental Escherichia coli population

Blount, Z. D., Barrick, J. E., Davidson, C. J., & Lenski, R. E. (2012) · Nature · doi:10.1038/nature11514 · Cited by 612

Alzheimer's disease as homeostatic responses to age-related myelin breakdown

Bartzokis, G. (2011) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2009.08.007 · Cited by 546

Modular cell biology: retroactivity and insulation

Del Vecchio, D., Ninfa, A. J., & Sontag, E. D. (2008) · Molecular Systems Biology · doi:10.1038/msb4100204 · Cited by 519

The new animal phylogeny: Reliability and implications

Adoutte, A., Balavoine, G., Lartillot, N., Lespinet, O., Prud'homme, B., & de Rosa, R. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.9.4453 · Cited by 512

Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene

Prud'homme, B., Gompel, N., Rokas, A., Kassner, V. A., Williams, T. M., Yeh, S.-D., True, J. R., & Carroll, S. B. (2006) · Nature · doi:10.1038/nature04597 · Cited by 507

Tracking footprints of artificial selection in the dog genome

Akey, J. M., Ruhe, A. L., Akey, D. T., Wong, A. K., Connelly, C. F., Madeoy, J., Nicholas, T. J., & Neff, M. W. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909918107 · Cited by 350

RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements

Brosius, J. (1999) · Gene · doi:10.1016/s0378-1119(99)00227-9 · Cited by 345

Minireview: Endocrine disruptors: Past lessons and future directions

Schug, T. T., Johnson, A. F., Birnbaum, L. S., Colborn, T., Guillette, L. J., Crews, D. P., Collins, T., Soto, A. M., vom Saal, F. S., McLachlan, J. A., et al. (2016) · Molecular Endocrinology · doi:10.1210/me.2016-1096 · Cited by 282

Bacterial Adaptation through Loss of Function

Hottes, A. K., Freddolino, L., Khare, A., Donnell, Z. N., Liu, J. C., & Tavazoie, S. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003617 · Cited by 270

The evolution of combinatorial gene regulation in fungi

Tuch, B. B., Galgoczy, D. J., Hernday, A. D., Li, H., & Johnson, A. D. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060038 · Cited by 228

Why is Brain Size so Important:Design Problems and Solutions as Neocortex Gets Biggeror Smaller

Kaas, J. H. (2000) · Brain and Mind · doi:10.1023/a:1010028405318 · Cited by 225

Multiple roles of the coding sequence 5′ end in gene expression regulation

Tuller, T., & Zur, H. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1313 · Cited by 206

How Robust Are Probabilistic Models of Higher-Level Cognition?

Marcus, G. F., & Davis, E. (2013) · Psychological Science · doi:10.1177/0956797613495418 · Cited by 195

Injury-Related Behavior and Neuronal Plasticity: an Evolutionary Perspective on Sensitization, Hyperalgesia, and Analgesia

Walters, E. T. (1994) · International Review of Neurobiology · doi:10.1016/s0074-7742(08)60307-4 · Cited by 206

Spatial embedding and wiring cost constrain the functional layout of the cortical network of rodents and primates

Horvát, S., Gămănuț, R., Ercsey-Ravasz, M., Magrou, L., Gămănuț, B., Van Essen, D. C., Burkhalter, A., Knoblauch, K., Toroczkai, Z., & Kennedy, H. (2016) · PLoS Biology · doi:10.1371/journal.pbio.1002512 · Cited by 198

De Novo Origin of Human Protein-Coding Genes

Wu, D.-D., Irwin, D. M., & Zhang, Y.-P. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002379 · Cited by 183

Gene sharing in lens and cornea: facts and implications

Piatigorsky, J. (1998) · Progress in Retinal and Eye Research · doi:10.1016/s1350-9462(97)00004-9 · Cited by 159

NODULE ROOT and COCHLEATA Maintain Nodule Development and Are Legume Orthologs of Arabidopsis BLADE-ON-PETIOLE Genes

Couzigou, J.-M., Zhukov, V., Mondy, S., Abu el Heba, G., Cosson, V., Ellis, T. H. N., Ambrose, M., Wen, J., Tadege, M., Tikhonovich, I., et al. (2012) · The Plant Cell · doi:10.1105/tpc.112.103747 · Cited by 145

The evolutionary ecology of technological innovations

Solée, R. V., Valverde, S., Casals, M. R., Kauffman, S. A., Farmer, D., & Eldredge, N. (2013) · Complexity · doi:10.1002/cplx.21436 · Cited by 140

The Evolution of Language: A Comparative Review

Fitch, W. T. (2005) · Biology & Philosophy · doi:10.1007/s10539-005-5597-1 · Cited by 137

Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia

Beeby, M., Ferreira, J. L., Tripp, P., Albers, S.-V., & Mitchell, D. R. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa006 · Cited by 110

Linear mitochondrial genomes: 30 years down the line

Nosek, J., Tomáška, L., Fukuhara, H., Suyama, Y., & Kováč, L. (1998) · Trends in Genetics · doi:10.1016/s0168-9525(98)01443-7 · Cited by 122

Beyond the pleistocene: Using phylogeny and constraint to inform the evolutionary psychology of human mating.

Eastwick, P. W. (2009) · Psychological Bulletin · doi:10.1037/a0016845 · Cited by 116

Spontaneous emergence of modularity in cellular networks

Solé, R. V., & Valverde, S. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2007.1108 · Cited by 102

Hormone signaling in evolution and development: a non-model system approachs

Heyland, A., Hodin, J., & Reitzel, A. M. (2005) · BioEssays · doi:10.1002/bies.20136 · Cited by 99

The Ribosome Challenge to the RNA World

Bowman, J. C., Hud, N. V., & Williams, L. D. (2015) · Journal of Molecular Evolution · doi:10.1007/s00239-015-9669-9 · Cited by 99

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life

Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-15 · Cited by 97

On the role of volume transmission and receptor-receptor interactions in social behaviour: focus on central catecholamine and oxytocin neurons

Fuxe, K., Borroto-Escuela, D. O., Romero-Fernandez, W., Ciruela, F., Manger, P., Leo, G., Díaz-Cabiale, Z., & Agnati, L. F. (2012) · Brain Research · doi:10.1016/j.brainres.2012.01.062 · Cited by 81

Lrat-specific domain facilitates Vitamin A metabolism by domain swapping in HRASLS3

Golczak, M., Sears, A. E., Kiser, P. D., & Palczewski, K. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1687 · Cited by 58

Evolutionary obstacles and not C–F bond strength make PFAS persistent

Wackett, L. P. (2024) · Microbial Biotechnology · doi:10.1111/1751-7915.14463 · Cited by 60

Urban tinkering

Elmqvist, T., Siri, J., Andersson, E., Anderson, P., Bai, X., Das, P. K., Gatere, T., Gonzalez, A., Goodness, J., Handel, S. N., et al. (2018) · Sustainability Science · doi:10.1007/s11625-018-0611-0 · Cited by 66

Co-opting evo-devo concepts for new insights into mechanisms of behavioural diversity

Hoke, K. L., Adkins-Regan, E., Bass, A. H., McCune, A. R., & Wolfner, M. F. (2019) · Journal of Experimental Biology · doi:10.1242/jeb.190058 · Cited by 42

De Novo Genes

Zhao, L., Svetec, N., & Begun, D. J. (2024) · Annual Review of Genetics · doi:10.1146/annurev-genet-111523-102413 · Cited by 38

Evolving complexity: how tinkering shapes cells, software and ecological networks.

Solé, R., & Valverde, S. (2020) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2019.0325 · Cited by 37

Fundamental constraints to the logic of living systems

Solé, R., Kempes, C. P., Corominas-Murtra, B., De Domenico, M., Kolchinsky, A., Lachmann, M., Libby, E., Saavedra, S., Smith, E., & Wolpert, D. (2024) · Interface Focus · doi:10.1098/rsfs.2024.0010 · Cited by 34

Towards an integrative theory of consciousness: Part 1 (Neurobiological and cognitive models)

De Sousa, A. (2013) · Mens Sana Monographs · doi:10.4103/0973-1229.109335 · Cited by 33

A Short History of Nearly Every Sense—The Evolutionary History of Vertebrate Sensory Cell Types

Schlosser, G. (2018) · Integrative and Comparative Biology · doi:10.1093/icb/icy024 · Cited by 33

The road to synthetic multicellularity

Solé, R., Ollé-Vila, A., Vidiella, B., Duran-Nebreda, S., & Conde-Pueyo, N. (2018) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2017.11.007 · Cited by 19

Possible genetic and epigenetic links between human inner speech, schizophrenia and altruism

Agnati, L. F., Barlow, P., Ghidoni, R., Borroto-Escuela, D. O., Guidolin, D., & Fuxe, K. (2012) · Brain Research · doi:10.1016/j.brainres.2012.02.074 · Cited by 29

Brains, Behaviour, and Cognition: Multiple Misconceptions

Font, E., Burghardt, G. M., & Leal, M. (2023) · Health and Welfare of Captive Reptiles · doi:10.1007/978-3-030-86012-7_7 · Cited by 24

Convergent Evolutionary Paths in Biological and Technological Networks

Solé, R. V., Valverde, S., & Rodriguez-Caso, C. (2011) · Evolution: Education and Outreach · doi:10.1007/s12052-011-0346-1 · Cited by 20

Do “Newly Born” orphan proteins resemble “Never Born” proteins? A study using three deep learning algorithms

Liu, J., Yuan, R., Shao, W., Wang, J., Silman, I., & Sussman, J. L. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26496 · Cited by 18

The Somatic Marker Hypothesis and Political Life

Verweij, M., & Damasio, A. (2019) · Oxford Research Encyclopedia of Politics · doi:10.1093/acrefore/9780190228637.013.928 · Cited by 15

The Rapid Evolution of De Novo Proteins in Structure and Complex

(2024) · doi:10.1093/gbe/evae107 · Cited by 13

An interview with Robert Lawler

Lawler, R. W., & Rushby, N. (2013) · British Journal of Educational Technology · doi:10.1111/j.1467-8535.2012.01372.x · Cited by 10