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Past and Present Environments
Journal of Evolutionary Psychology, 2011, 275-278 DOI: 10.1556/JEP.9.2011.3.5 PAST AND PRESENT ENVIRONMENTS A review of Decision Making: Towards an Evolutionary Psychology of Rationality, by Mauro Maldonato. Sussex Academic Press (2010), 121 pages, $32.50. ISBN: 978-1-84519-421-5 (paperback) 1 2 CHELSEA ROSS AND ANDREAS WILKE Department of Psychology, Clarkson University In his book, Maldonato provides a thoughtful look at how early scholars viewed de- cision-making and rationality. He takes the reader on an illustrative journey through the historic passages of decision-making all the way to modern notions of a more limited rationality and how humans can make choices under risk and uncertainty. He discusses Kahneman and Tversky’s seminal work on heuristics and biases— “short cuts” that rely on little information and modest cognitive resources that sometimes lead to persistent failures, but usually allow the decision-maker to make fast and fairly reliable choices. Herbert Simon and Gerd Gigerenzer’s work on bounded rationality is discussed, with respect to its influence on decision-making research in economics and psychology. For Maldonato, the principle of bounded ra- tionality—that organisms have limited resources, such as time, information, and cognitive capacity with which to find solutions to the problems they face—is a key insight to understanding the evolution of decision-making. Maldonato proposes that evolutionary pressures urged the human mind to adopt a primitive decision-making process. For the purpose of survival, the majority of human choices had to be made by means of simple and fast decision strategies, because the decision-making system developed under general human cognitive limitations and from environmental pressures that selected for decision strategies suited for the harsh ancestral living environments as well as the resources at hand. -
The University of Chicago Epistasis, Contingency, And
THE UNIVERSITY OF CHICAGO EPISTASIS, CONTINGENCY, AND EVOLVABILITY IN THE SEQUENCE SPACE OF ANCIENT PROTEINS A DISSERTATION SUBMITTED TO THE FACULTY OF THE DIVISION OF THE BIOLOGICAL SCIENCES AND THE PRITZKER SCHOOL OF MEDICINE IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN BIOCHEMISTRY AND MOLECULAR BIOPHYSICS BY TYLER NELSON STARR CHICAGO, ILLINOIS AUGUST 2018 Table of Contents List of Figures .................................................................................................................... iv List of Tables ..................................................................................................................... vi Acknowledgements ........................................................................................................... vii Abstract .............................................................................................................................. ix Chapter 1 Introduction ......................................................................................................1 1.1 Sequence space and protein evolution .............................................................1 1.2 Deep mutational scanning ................................................................................2 1.3 Epistasis ...........................................................................................................3 1.4 Chance and determinism ..................................................................................4 1.5 Evolvability ......................................................................................................6 -
What Can We Learn from Fitness Landscapes?
What can we learn from fitness landscapes? The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Hartl, Daniel L. 2014. “What Can We Learn from Fitness Landscapes?” Current Opinion in Microbiology 21 (October): 51–57. doi:10.1016/j.mib.2014.08.001. Published Version 10.1016/j.mib.2014.08.001 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:22898356 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP Elsevier Editorial System(tm) for Current Opinion in Microbiology Manuscript Draft Manuscript Number: Title: What Can We Learn From Fitness Landscapes? Article Type: 22 Growth&Develop: prokaryotes (2014 Corresponding Author: Dr. Daniel Hartl, Corresponding Author's Institution: First Author: Daniel Hartl Order of Authors: Daniel Hartl Manuscript Click here to view linked References What Can We Learn From Fitness Landscapes? Daniel L. Hartl Department of Organismic and Evolutionary Biology Harvard University Cambridge, Massachusetts 02138 USA Contact information: Email: [email protected], TEL: 617-396-3917 In evolutionary biology, the fitness landscape of set of mutants is the mapping of genotypes onto phenotypes when the phenotype is fitness or some proxy for fitness such as growth rate or drug resistance. When the set of mutants is not too large, it is possible to create every possible combination of mutants and map these to fitness. -
Information Systems Theorizing Based on Evolutionary Psychology: an Interdisciplinary Review and Theory Integration Framework1
Kock/IS Theorizing Based on Evolutionary Psychology THEORY AND REVIEW INFORMATION SYSTEMS THEORIZING BASED ON EVOLUTIONARY PSYCHOLOGY: AN INTERDISCIPLINARY REVIEW AND THEORY INTEGRATION FRAMEWORK1 By: Ned Kock on one evolutionary information systems theory—media Division of International Business and Technology naturalness theory—previously developed as an alternative to Studies media richness theory, and one non-evolutionary information Texas A&M International University systems theory, channel expansion theory. 5201 University Boulevard Laredo, TX 78041 Keywords: Information systems, evolutionary psychology, U.S.A. theory development, media richness theory, media naturalness [email protected] theory, channel expansion theory Abstract Introduction Evolutionary psychology holds great promise as one of the possible pillars on which information systems theorizing can While information systems as a distinct area of research has take place. Arguably, evolutionary psychology can provide the potential to be a reference for other disciplines, it is the key to many counterintuitive predictions of behavior reasonable to argue that information systems theorizing can toward technology, because many of the evolved instincts that benefit from fresh new insights from other fields of inquiry, influence our behavior are below our level of conscious which may in turn enhance even more the reference potential awareness; often those instincts lead to behavioral responses of information systems (Baskerville and Myers 2002). After that are not self-evident. This paper provides a discussion of all, to be influential in other disciplines, information systems information systems theorizing based on evolutionary psych- research should address problems that are perceived as rele- ology, centered on key human evolution and evolutionary vant by scholars in those disciplines and in ways that are genetics concepts and notions. -
Phenotypic Landscape Inference Reveals Multiple Evolutionary Paths to C4 Photosynthesis
RESEARCH ARTICLE elife.elifesciences.org Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis Ben P Williams1†, Iain G Johnston2†, Sarah Covshoff1, Julian M Hibberd1* 1Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom; 2Department of Mathematics, Imperial College London, London, United Kingdom Abstract C4 photosynthesis has independently evolved from the ancestral C3 pathway in at least 60 plant lineages, but, as with other complex traits, how it evolved is unclear. Here we show that the polyphyletic appearance of C4 photosynthesis is associated with diverse and flexible evolutionary paths that group into four major trajectories. We conducted a meta-analysis of 18 lineages containing species that use C3, C4, or intermediate C3–C4 forms of photosynthesis to parameterise a 16-dimensional phenotypic landscape. We then developed and experimentally verified a novel Bayesian approach based on a hidden Markov model that predicts how the C4 phenotype evolved. The alternative evolutionary histories underlying the appearance of C4 photosynthesis were determined by ancestral lineage and initial phenotypic alterations unrelated to photosynthesis. We conclude that the order of C4 trait acquisition is flexible and driven by non-photosynthetic drivers. This flexibility will have facilitated the convergent evolution of this complex trait. DOI: 10.7554/eLife.00961.001 Introduction *For correspondence: Julian. The convergent evolution of complex traits is surprisingly common, with examples including camera- [email protected] like eyes of cephalopods, vertebrates, and cnidaria (Kozmik et al., 2008), mimicry in invertebrates and †These authors contributed vertebrates (Santos et al., 2003; Wilson et al., 2012) and the different photosynthetic machineries of equally to this work plants (Sage et al., 2011a). -
Quantifying the Fitness of Tissue-Specific Evolutionary
bioRxiv preprint doi: https://doi.org/10.1101/401059; this version posted August 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Quantifying the fitness of tissue- specific evolutionary trajectories by harnessing cancer’s repeatability at the genetic level Tokutomi N1, Moyret-Lalle C2, Puisieux A2, Sugano S1, Martinez P2. 1 Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan. 2 Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France, INSERM U1052, Cancer Research Center of Lyon, Lyon, F-69008, France. Correspondence to Pierre Martinez: [email protected] Abstract Cancer is a potentially lethal disease, in which patients with nearly identical genetic backgrounds can develop a similar pathology through distinct combinations of genetic alterations. We aimed to reconstruct the evolutionary process underlying tumour initiation, using the combination of convergence and discrepancies observed across 2,742 cancer genomes from 9 tumour types. We developed a framework using the repeatability of cancer development to score the fitness of genetic clones, as their potential to malignantly progress and invade their environment of origin. Using this framework, we found that pre-malignant skin and colorectal lesions appeared specifically adapted to their local environment, yet insufficiently for full cancerous transformation. We found that metastatic clones were more adapted to the site of origin than to the invaded tissue, suggesting that genetics may be more important for local progression than for the invasion of distant organs. -
Evolutionary Genetics
Evolutionary Genetics Ruben C. Arslan & Lars Penke Institute of Psychology Georg August University Göttingen Forthcoming in D. M. Buss (Ed.), Handbook of Evolutionary Psychology (2nd ed.). New York: Wiley. September 17, 2014 Corresponding author: Ruben C. Arslan Georg August University Göttingen Biological Personality Psychology and Psychological Assessment Georg Elias Müller Institute of Psychology Goßlerstr. 14 37073 Göttingen, Germany Tel.: +49 551 3920704 Email: [email protected] 1 Introduction When Charles Darwin developed the theory of evolution, he knew nothing about genetics. Hence, one of its biggest weaknesses was that Darwin had to base it on crude ideas of inheritance. Around the same time, Gregor Mendel discovered the laws of inheritance, but the scientific community initially failed to appreciate his work’s importance. It was only in the 1930’s that Dobzhansky, Fisher, Haldane, Wright, Mayr and others unified genetics and the theory of evolution in the ‘modern synthesis’. Still, the modern synthesis was built on a basic understanding of genetics, with genes merely being particulate inherited information. The basics of molecular genetics, like the structure of DNA, were not discovered until the 1950’s. When modern evolutionary psychology emerged from ethology and sociobiology in the late 1980’s, it had a strong emphasis on human universals, borne from both the assumption that complex adaptations are monomorphic (or sexually dimorphic) and have to go back to at least the last common ancestor of all humans, and the methodological proximity to experimental cognitive psychology, which tends to treat individual differences as statistical noise. As a consequence, genetic differences between people were marginalized in evolutionary psychology (Tooby & Cosmides, 1990). -
Correction for Barua and Mikheyev, an Ancient, Conserved Gene Regulatory Network Led to the Rise of Oral Venom Systems
Correction EVOLUTION Correction for “An ancient, conserved gene regulatory network led to the rise of oral venom systems,” by Agneesh Barua and Alexander S. Mikheyev, which was first published March 29, 2021; 10.1073/pnas.2021311118 (Proc. Natl. Acad. Sci. U.S.A. 118, e2021311118). The editors note that, due to a printer’s error, the article in- advertently published with a number of language errors. The article has been updated online to correct these errors. Published under the PNAS license. Published May 24, 2021. www.pnas.org/cgi/doi/10.1073/pnas.2108106118 CORRECTION PNAS 2021 Vol. 118 No. 22 e2108106118 https://doi.org/10.1073/pnas.2108106118 | 1of1 Downloaded by guest on October 1, 2021 An ancient, conserved gene regulatory network led to the rise of oral venom systems Agneesh Baruaa,1 and Alexander S. Mikheyeva,b aEcology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495, Japan; and bEvolutionary Genomics Group, Australian National University, Canberra, ACT 0200, Australia Edited by Günter P. Wagner, Yale University, New Haven, CT, and approved February 11, 2021 (received for review October 27, 2020) Oral venom systems evolved multiple times in numerous verte- over time; this diminishes their utility in trying to understand brates, enabling the exploitation of unique predatory niches. Yet events that lead to the rise of venom systems in the nonvenom- how and when they evolved remains poorly understood. Up to ous ancestors of snakes (14, 15). now, most research on venom evolution has focused strictly on A gene coexpression network aims to identify genes that in- toxins. -
S41467-017-02329-Y.Pdf
ARTICLE DOI: 10.1038/s41467-017-02329-y OPEN The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy Dan A. Landau1,2,3, Clare Sun 4, Daniel Rosebrock2, Sarah E.M. Herman4, Joshua Fein1,3,5, Mariela Sivina6, Chingiz Underbayev4, Delong Liu4, Julia Hoellenriegel6, Sarangan Ravichandran7, Mohammed Z.H. Farooqui4, Wandi Zhang8, Carrie Cibulskis2, Asaf Zviran1,3, Donna S. Neuberg 9, Dimitri Livitz 2, Ivana Bozic10, Ignaty Leshchiner 2, Gad Getz 2, Jan A. Burger6, Adrian Wiestner4 & Catherine J. Wu2,8,11 1234567890 Treatment of chronic lymphocytic leukemia (CLL) has shifted from chemo-immunotherapy to targeted agents. To define the evolutionary dynamics induced by targeted therapy in CLL, we perform serial exome and transcriptome sequencing for 61 ibrutinib-treated CLLs. Here, we report clonal shifts (change >0.1 in clonal cancer cell fraction, Q < 0.1) in 31% of patients during the first year of therapy, associated with adverse outcome. We also observe tran- scriptional downregulation of pathways mediating energy metabolism, cell cycle, and B cell receptor signaling. Known and previously undescribed mutations in BTK and PLCG2,or uncommonly, other candidate alterations are present in seventeen subjects at the time of progression. Thus, the frequently observed clonal shifts during the early treatment period and its potential association with adverse outcome may reflect greater evolutionary capacity, heralding the emergence of drug-resistant clones. 1 New York Genome Center, New York, NY 10013, USA. 2 Broad Institute, Cambridge, MA 02142, USA. 3 Meyer Cancer Center & Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA. 4 Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. -
Evolutionary Psychology in the Service of Moral Psychology: a Possible Future for Ethics William S
Skidmore College Creative Matter Philosophy Faculty Scholarship Philosophy Department 2011 Evolutionary Psychology in the Service of Moral Psychology: A Possible Future for Ethics William S. Lewis Skidmore College Follow this and additional works at: https://creativematter.skidmore.edu/phil_rel_fac_schol Part of the Philosophy Commons Recommended Citation Lewis, W. S. (2011). Evolutionary Psychology in the Service of Moral Philosophy: A Possible Future for Ethics?. Journal Of Speculative Philosophy, 25(1), 48-63. This Article is brought to you for free and open access by the Philosophy Department at Creative Matter. It has been accepted for inclusion in Philosophy Faculty Scholarship by an authorized administrator of Creative Matter. For more information, please contact [email protected]. Evolutionary Psychology in the Service of Moral Philosophy, A Possible Future for Ethics? William S. Lewis Skidmore College Draft of “Evolutionary Psychology in the Service of Moral Psychology: A Possible Future for Ethics.” Journal of Speculative Philosophy Vol. 25, No. 1 (2011): 48-63. “Someone may ask, “What is the difference, then, between moral philosophy and moral psychology?” The answer may be that there is no interesting difference and that the issue is of interest only to university administrators.”1 In “The Moral Philosopher and the Moral Life (1891),” William James provides a rough taxonomy of the state of ethical philosophy at the time that he is writing. Making a division between psychological approaches that identify the good with the feeling of pleasure derived by a naturally evolved organism and metaphysical approaches which hold that the good is conceptual, James argues that both are equally goods and that they each imply similar obligation. -
Exaptation, Adaptation, and Evolutionary Psychology
Exaptation, Adaptation, and Evolutionary Psychology Armin Schulz Department of Philosophy, Logic, and Scientific Method London School of Economics and Political Science Houghton St London WC2A 2AE UK [email protected] (0044) 753-105-3158 Abstract One of the most well known methodological criticisms of evolutionary psychology is Gould’s claim that the program pays too much attention to adaptations, and not enough to exaptations. Almost as well known is the standard rebuttal of that criticism: namely, that the study of exaptations in fact depends on the study of adaptations. However, as I try to show in this paper, it is premature to think that this is where this debate ends. First, the notion of exaptation that is commonly used in this debate is different from the one that Gould and Vrba originally defined. Noting this is particularly important, since, second, the standard reply to Gould’s criticism only works if the criticism is framed in terms of the former notion of exaptation, and not the latter. However, third, this ultimately does not change the outcome of the debate much, as evolutionary psychologists can respond to the revamped criticism of their program by claiming that the original notion of exaptation is theoretically and empirically uninteresting. By discussing these issues further, I also seek to determine, more generally, which ways of approaching the adaptationism debate in evolutionary biology are useful, and which not. Exaptation, Adaptation, and Evolutionary Psychology Exaptation, Adaptation, and Evolutionary Psychology I. Introduction From a methodological point of view, one of the most well known accusations of evolutionary psychology – the research program emphasising the importance of appealing to evolutionary considerations in the study of the mind – is the claim that it is overly “adaptationist” (for versions of this accusation, see e.g. -
Evolutionary Ethics? Substantiators, Skeptics, and Moral Realism
University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2013-04-30 Evolutionary Ethics? Substantiators, Skeptics, and Moral Realism Jimenez, Kieran Chad Jimenez, K. C. (2013). Evolutionary Ethics? Substantiators, Skeptics, and Moral Realism (Unpublished master's thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/26002 http://hdl.handle.net/11023/662 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Evolutionary Ethics? Substantiators, Skeptics, and Moral Realism by Kieran Jimenez A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF ARTS DEPARTMENT OF POLITICAL SCIENCE CALGARY, ALBERTA APRIL, 2013 © Kieran Jimenez 2013 Abstract Hardly a week passes without new findings emerging from evolutionary psychology regarding how our view of morality has been influenced by our biological evolution. Evolutionary ethics is a normative project built upon these scientific insights. Evolutionary ethicists fall into two groups: substantiators or skeptics. Substantiators believe moral ideas can now be scientifically proven. Skeptics believe there are no moral truths because morality is just a biological adaptation. I believe the project of evolutionary ethics is misconceived. I argue that both the substantiators and the skeptics fail to show the direct relevance of biology to ethics.