Self-Organization of Biological Systems
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Evolution of Complexity in Real-World Domains
Evolution of Complexity in Real-World Domains A Dissertation Presented to The Faculty of the Graduate School of Arts and Sciences Brandeis University Department of Computer Science Jordan B. Pollack, Advisor In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy by Pablo Funes May, 2001 This dissertation, directed and approved by Pablo Funes’s committee, has been accepted and approved by the Graduate Faculty of Brandeis University in partial fulfillment of the requirements for the degree of: DOCTOR OF PHILOSOPHY Dean of Arts and Sciences Dissertation Committee: Jordan B. Pollack, Dept. of Computer Science, Chair. Martin Cohn, Dept. of Computer Science Timothy J. Hickey, Dept. of Computer Science Dario Floreano, ISR, École Polytechnique Fédérale de Lausanne c Copyright by Pablo Funes 2001 in memoriam Everé Santiago Funes (1913-2000) vii Acknowledgments Elizabeth Sklar collaborated on the work on coevolving behavior with live creatures (chapter 3). Hugues Juillé collaborated with the Tron GP architecture (section 3.3.3) and the nov- elty engine (section 3.3.7). Louis Lapat collaborated on EvoCAD (section 2.9). Thanks to Jordan Pollack for the continuing support and for being there when it really matters. Thanks to Betsy Sklar, my true American friend. And to Richard Watson for the love and the focus on the real science. Also to all the people who contributed in one way or another, in no particular order: José Castaño, Adriana Villella, Edwin De Jong, Barry Werger, Ofer Melnik, Isabel Ennes, Sevan Ficici, Myrna Fox, Miguel Schneider, Maja Mataric, Martin Cohn, Aroldo Kaplan, Otilia Vainstok. And mainly to my family and friends, among them: María Argüello, Santiago Funes, Soledad Funes, Carmen Argüello, María Josefa González, Faustino Jorge, Martín Leven- son, Inés Armendariz, Enrique Pujals, Carlos Brody, Ernesto Dal Bo, Martín Galli, Marcelo Oglietti. -
'Are You Playing God?': Synthetic Biology and the Chemical Ambition
‘Are You Playing God?’: Synthetic Biology and the Chemical Ambition to Create Artificial Life Joachim Schummer Abstract : Throughout history chemists have faced the accusation of ‘playing God’ or similar devilish associations, overshadowing all moral judgments of chemistry. The paper provides an ethical analysis of the accusation with focus on Craig Venter’s 2010 announcement of having produced the ‘first self- replicating cell’. Against the deeper historical background of the ambitious projects that came to be known as ‘synthetic biology’, I describe Venter’s ac- tual research and its international media reception. Then I analyze both the ethical and theological implications of creating living beings in the laboratory. In conclusion I argue that the Venter case, like many others cases from chem- istry before, is a case of unfortunate science-public interaction that mislead both ethics and science. Keywords : ethics of chemistry, synthetic biology, artificial life, playing God, pub- lic image of chemistry . 1. Introduction Chemists working on apparently innocent research projects might be sur- prised if not puzzled when they suddenly face the public accusation of ‘play- ing God’. They probably think: ‘I am just doing good science for the benefit of society. How is that related to religion? Why should that be bad?’ Much more than any other science, chemistry carries a heritage of reli- gious presumption and hubris continuing over 2,000 years. Responsible chemists should be particularly aware of their cultural history, cautious about societal provocations and pitfalls, and versed in ethics. In the Christian tradition, the accusation of ‘playing God’ was originally applied to the ‘Fallen Angels’ who would later be called devils under the lead- ership of Satan. -
The Creation of Life in Cultural Context: from Spontaneous
To be published in Mark Bedau & Emily Parke (eds.): Our Future with Protocells: The Social and Ethical Implications of the Creation of Living, Cambridge, MA: MIT Press, 2007. The Creation of Life in Cultural Context: From Spontaneous Generation to Synthetic Biology Joachim Schummer Department of Philosophy, University of Darmstadt; [email protected] 1. Introduction The artificial creation of life arises both strong fascination by scientists and strong concerns, if not abhorrence, by critics of science. What appears to be the crowning achievement of syn- thetic biology is at the same time considered a major evil. That conflict, which perhaps epitomizes many of the cultural conflicts about science in Western societies, calls for a deeper analysis. Standard ethical analyses, which would try to relate such conflicts to a difference in fundamental values, are difficult to apply here, because it is unclear what the underlying val- ues of such emotions as fascination and abhorrence are. These emotions or affects, rather than just referring to what is morally right or wrong, seem to be rooted in our cultural heritage of desires and taboos of transgression. My analysis in this paper is primarily of historical nature. By investigating ideas about the creation of life from the earliest times to the present, I aim to clarify the cultural origins of those emotions. I argue that both the fascination and the abhorrence regarding the creation of life have a common religious basis. Moreover, unlike many commentators of 19th-century mad-scientist classics, from Mary Shelley to H.G. Wells, I argue that this basis has no ancient model in religious or mythological traditions but emerged only in the 19th century from an exchange between science and religion. -
The Artificial Creation of Life and What It Means to Be Human Caroline Mosser University of South Carolina
University of South Carolina Scholar Commons Theses and Dissertations 6-30-2016 The Artificial Creation Of Life And What It Means To Be Human Caroline Mosser University of South Carolina Follow this and additional works at: https://scholarcommons.sc.edu/etd Part of the Arts and Humanities Commons Recommended Citation Mosser, C.(2016). The Artificial Creation Of Life And What It Means To Be Human. (Doctoral dissertation). Retrieved from https://scholarcommons.sc.edu/etd/3482 This Open Access Dissertation is brought to you by Scholar Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. The Artificial Creation of Life and What It Means to Be Human by Caroline Mosser Bachelor of Arts Upper Alsace University, 2009 Master of Arts Upper Alsace University, 2011 Submitted in Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy in Comparative Literature College of Arts and Sciences University of South Carolina 2016 Accepted by: Daniela Di Cecco, Major Professor Yvonne Ivory, Committee Member Rebecca Stern, Committee Member Susan Vanderborg, Committee Member Lacy Ford, Senior Vice Provost and Dean of Graduate Studies © Copyright by Caroline Mosser, 2016 All Rights Reserved ii Acknowledgements I would like to express my gratitude to those who have supported me throughout my graduate studies, leading to the present dissertation. First and foremost, I would like to thank my advisor, Dr. Daniela Di Cecco for her continuous support, patience, and guidance throughout this project. Her technical and editorial advice was essential for its completion. -
Reproductive Imaginations in German Culture by Annika Orich A
Artificial Aliens: Reproductive Imaginations in German Culture by Annika Orich A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in German and the Designated Emphasis in Film Studies in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Deniz Göktürk, Chair Professor Anton Kaes Professor Abigail De Kosnik Fall 2017 Abstract Artificial Aliens: Reproductive Imaginations in German Culture by Annika Orich Doctor of Philosophy in German Designated Emphasis in Film Studies University of California, Berkeley Professor Deniz Göktürk, Chair This dissertation, titled “Artificial Aliens: Reproductive Imaginations in German Culture,” studies how reproductive processes in biology and the arts evoke similar cultural anxieties, and how they, in turn, are shaped by these same fears. I view and investigate reproduction in biology and the arts as related processes, specifically those conducted via artificial means. My dissertation examines this relationship by tracing artificial aliens as a point of connection across disciplines, media, and periods. The figure of the artificial alien appears as artificial human, othered stranger, alien lifeform, and cinematic image. I develop my argument via several case studies, ranging from Weimar silent films such as Otto Rippert’s Homunculus (1916/1920) and Henrik Galeen’s Alraune (1927/1928) to Frank Schätzing’s science fiction bestseller Der Schwarm (2004) to Netflix’s original series Sense8 (2015-). I argue that there exists a complex dynamic between reproductive processes in biology and the arts and discourses on memory, identity, and media and its archaeology. This project thus contributes to existing research on the interplay between science and fiction. -
Evolutionary Algorithms: Concepts, Designs, and Applications in Bioinformatics Evolutionary Algorithms for Bioinformatics
Evolutionary Algorithms: Concepts, Designs, and Applications in Bioinformatics Evolutionary Algorithms for Bioinformatics Ka-Chun Wong Department of Computer Science, University of Toronto, Ontario, Canada INTRODUCTION Since genetic algorithm was proposed by John Holland (Holland J. H., 1975) in the early 1970s, the study of evolutionary algorithm has emerged as a popular research field (Civicioglu & Besdok, 2013). Researchers from various scientific and engineering disciplines have been digging into this field, exploring the unique power of evolutionary algorithms (Hadka & Reed, 2013). Many applications have been successfully proposed in the past twenty years. For example, mechanical design (Lampinen & Zelinka, 1999), electromagnetic optimization (Rahmat-Samii & Michielssen, 1999), environmental protection (Bertini, Felice, Moretti, & Pizzuti, 2010), finance (Larkin & Ryan, 2010), musical orchestration (Esling, Carpentier, & Agon, 2010), pipe routing (Furuholmen, Glette, Hovin, & Torresen, 2010), and nuclear reactor core design (Sacco, Henderson, Rios-Coelho, Ali, & Pereira, 2009). In particular, its function optimization capability was highlighted (Goldberg & Richardson, 1987) because of its high adaptability to different function landscapes, to which we cannot apply traditional optimization techniques (Wong, Leung, & Wong, 2009). BACKGROUND Evolutionary algorithms draw inspiration from nature. An evolutionary algorithm starts with a randomly initialized population. The population then evolves across several generations. In each generation, -
Lear-Headed About What Artificial Life Research Does and Does Not Do, and Not to Be Confused by Ontological Misconceptions and Misleading Terminology
Uploaded March 10, 1998 Volume 6, Number 2 Life as We Know It and/or Life as It Could Be: Epistemology and the Ontology/Ontogeny of Artificial Life1 Edward A. Shanken I. "...nature as described by our scientists is indeed an artifact built in collaboration with a Being sufficiently complex to mock and, perhaps, punish materialists by responding to them in a crudely materialistic way..." - Paul Feyerabend, Nature as a Work of Art 2 Feyerabend's point is not that materialists are dim-witted and circular and get what they deserve, but that any given scientific explanation will be partial at best. It will function well in certain domains, and poorly in others - where alternative, perhaps incommensurable explanations, will do the trick. As a result, he likens the artwork of science to the constructions of Kurt Schwitters, such as the German artist's merzbild Konstruction für edle Frauen (Construction for Noble Ladies, 1919) (http:// lonestar.texas.net/~mharden/artchive/S/schwitters.html), which the philosopher characterizes as an ad- hoc cobbling together of found objects in an amorphous structure. Noting that when "approached in different ways Nature gives different responses," Feyerabend concludes that universal explanations of nature-in-itself appear dubious. He proposes that science, which tends to search for unequivocal, unambiguous answers, could benefit from the arts, whose subtle understanding and appreciation of paradox and absurdity might complement what he calls the " 'objective' artifact nature."3 Implicit in the comments above is the idea that science is a hermeneutic rather than teleological endeavor. Artificial Life, as the conjunction of biology and computational science, is likewise an interpretive discipline, one which - due to the domain of its inquiry and the nature and extent of its claims - raises many gnarly epistemological and ontological questions. -
SIGEVO Newsletter
Autumn 2007 SIGEVOlution Volume 2 Issue 3 newsletter of the ACM Special Interest Group on Genetic and Evolutionary Computation in this issue GA @ The WSC Vincent de Geus & the 2007 Nuon Solar Team Buildable Evolution Pablo Funes What is an LCS? Stewart W. Wilson The Columns dissertation corner new issues of journals calls & calendar EDITORIAL SIGEVOlution Autumn 2007, Volume 2, Issue 3 Newsletter of the ACM Special Interest Group Editorial on Genetic and Evolutionary Computation. solar car hisses through the beautiful Australian desert; its racing strategy has been evolved SIGEVO Officers using a genetic algorithm. Meanwhile, in a university laboratory, Lego structures are evolved Darrell Whitley, Chair using Genetic Programming. Indeed, this new issue of SIGEVOlution shows some rather un- John Koza, Vice Chair A usual applications of evolutionary computation and I hope you will enjoy reading it! Erick Cantu-Paz, Secretary Wolfgang Banzhaf, Treasurer In the first paper, Vincent de Geus and the Nuon team from the Delft University of Technology tell us how they applied a genetic algorithm to optimize the racing strategy for their solar car leading them SIGEVOlution Board to win the World Solar Challenge. In the second paper, Pablo Funes shows us how we can evolve Lego structures using Genetic Programming while, in the third and last paper, Stewart Wilson provides a gentle Pier Luca Lanzi (EIC) introduction to accuracy-based classifier systems. The subsequent columns provide information about a Lawrence "David" Davis recently discussed PhD thesis, the new issues of EC journals, and the calendar of EC events. Martin Pelikan The cover photo is by Hans-Peter van Velthoven. -
Synthetic Biology Is the Bundestag.De/En/Research/U9800
FOCUS: HOPE, HYPE AND FEAR TECHNOLOGIES SYNTHETIC BIOLOGY: FINAL TECHNOLOGISATION OF LIFE – OR NO NEWS AT ALL? Synthetic biology currently represents a prime example of a »hope, hype and fear > Construction of chemical systems technology«. On the one hand, it has a close methodological connection with (new biomolecules) corresponding genetic engineering while, on the other hand, being close to nanotechnology to biological models such that these and converging technologies in discursive terms. Even though there is as yet no systems manifest certain properties consensus about the essence and prospects of synthetic biology, it is regarded of living organisms by many as the key direction in which developments are heading in biosciences > Reduction of organisms to rudi- – with the latter being seen in turn as the defining science of the 21st century, mentary system components by following in the footsteps of physics in the 19th century and chemistry in installing standardised modular the 20th. This paper will show that a certain discrepancy can be identified biological parts (›BioBricks‹) for between the extent of the expectations, hopes and fears under discussion the purpose of creating biological TAB-BRIEF NR. 39 / SPECIAL EDITION and the available fund of knowledge or of specifically foreseeable potential circuits that respond to external applications. stimuli« This description deliberately avoids an One characteristic feature of hope, The understanding which forms the advance positioning on the news value hype and fear technologies, without basis for the current TAB project on of synthetic biology and serves as a doubt, is that every debate about synthetic biology has been defined starting point so that, as a result of it is preceded by a discussion of as follows (http://www.tab-beim- the systematic capture of application its definition or whether there is a bundestag.de/en/research/u9800.