So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

Principles of Neural Science

Language, Thought, and Other Biological Categories

A clutch of '-isms' characterises the approach to consciousness which David Chalmers defends: dualism, epiphenomenalism, functionalism, anti-reductionism, and -probably -panpsychism. (The author would no doubt want 'naturalism' included in the list as well, but as we shall see, Chalmers' predilection to describe his theory as 'scientific' stretches credibility.) While the book does not, as far as I can see, move consciousness research significantly forward, Chalmers succeeds admirably in clarifying the philosophical terrain around and within each of these '-isms' and in questioning the usual assumptions which suggest some of them are mutually exclusive. Because nearly all of what follows is highly critical, I want to be explicit about one thing: I do not think this is a bad book. Throughout, most discussions keep to a very high standard; it's just that they include fatal flaws.

The conscious mind: In search of a fundamental theory

THE purpose of this work, which the authors regard as a pioneer attempt, is the accomplishment in the field of masculinity and femininity of something similar to Binet's early achievement in the field of intelligence, inasmuch as they have endeavoured to apply psychometric methods in the form of a test to the study of sex temperaments. The test was originally devised by the senior author, Lewis M. Terman, in 1922 in the investigation of intellectually superior children, and has since been applied in the examination of a great variety of groups, including college students, office workers, athletes, delinquents, homosexuals and prostitutes, the ages ranging from early adolescence to extreme old age.Sex and Personality': Studies in Masculinity and Femininity. By Lewis M. Terman and Catherine Cox Miles., assisted by Jack W. Dunlap, Harold K. Edgerton, E. Lowell Kelly, Albert D. Kurtz, E. Alice McAnulty, Quinn McNemar, Maud A. Merrill, Floyd L. Ruch, Horace G. Wyatt. (McGraw-Hill Publications in Psychology.) Pp. xii + 600. (New York and London: McGraw-Hill Book Co., Inc., 1936.) 25s.

Sex and personality

In the era of "big data," science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use.After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.

/pdf/building-ontologies-with-basic-formal-ontology-3owenvzu1h.pdf

Building Ontologies with Basic Formal Ontology

Numerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three BFO categories of function, role, and disposition, and considers two proposed sub-categories of artifactual function and bio-logical function. The motivation is to help advance the coherent treatment of functions, roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general structure and use.

/pdf/function-role-and-disposition-in-basic-formal-ontology-1tgcqt2ie3.pdf

Function, Role and Disposition in Basic Formal Ontology

Notes on Contributors General Introduction References and Further Reading Part I: Is It Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics? Introduction References and Further Reading 1. It Is Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics: Evelyn Fox Keller (MIT) 2. It Is Not Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics: John Dupre (University of Exeter) Part II: Have Traits Evolved to Function the Way They Do Because of a Past Advantage? Introduction References and Further Reading 3. Traits Have Evolved to Function the Way They Do Because of a Past Advantage: Mark Perlman (Western Oregon University) 4. Traits Have Not Evolved to Function the Way They Do Because of a Past Advantage: Robert Cummins (University of Illinois-Urbana-Champagin) and Martin Roth (Drake University) Part III: Are Species Real? Introduction References and Further Reading 5. Species Are Real Biological Entities: Michael F. Claridge (Cardiff University) 6. Species Are Not Uniquely Real Biological Entities: Brent D. Mishler (University of California-Berkeley) Part IV: Does Selection Operate Primarily on Genes? Introduction References and Further Reading 7. Selection Does Operate Primarily on Genes: In Defense of the Gene as the Unit of Selection: Carmen Sapienza (Temple University) 8. Selection Does Not Operate Primarily on Genes: Richard M. Burian (University of Pittsburgh) Part V: Are Microevolution and Macroevolution Governed by the Same Processes? Introduction References and Further Reading 9. Microevolution and Macroevolution Are Governed by the Same Processes: Michael R. Dietrich (Dartmouth College) 10. Microevolution and Macroevolution Are Not Governed by the Same Processes: Douglas H. Erwin (Smithsonian Institution and Santa Fe Institute) Part VI: Does Evolutionary Developmental Biology Offer a Significant Challenge to the Neo-Darwinian Paradigm? Introduction References and Further Reading 11. Evolutionary Developmental Biology Does Offer a Significant Challenge to the Neo-Darwinian Paradigm: Manfred D. Laubichler (Arizona State University) 12. Evolutionary Developmental Biology Does Not Offer a Significant Challenge to the Neo-Darwinian Paradigm: Alessandro Minelli (University of Padova) Part VII: Were the Basic Components of the Human Mind Solidified During the Pleistocene Epoch? Introduction References and Further Reading 13. The Basic Components of the Human Mind Were Solidified During the Pleistocene Epoch: Valerie G. Starratt (Nova Southeastern University) and Todd K. Shackelford (Florida Atlantic University) 14. The Basic Components of the Human Mind Were Not Solidified During the Pleistocene Epoch: Stephen M. Downes (University of Utah) Part VIII: Does Memetics Provide a Useful Way of Understanding Cultural Evolution? Introduction References and Further Reading 15. Memetics Does Provide a Useful Way of Understanding Cultural Evolution: Susan Blackmore (University of the West of England) 16. Memetics Does Not Provide a Useful Way of Understanding Cultural Evolution: A Developmental Perspective: William C. Wimsatt (University of Chicago) Part IX: Can the Biological Sciences Act as a Ground for Ethics? Introduction References and Further Reading 17. The Biological Sciences Can Act as a Ground for Ethics: Michael Ruse (Florida State University) 18. What the Biological Sciences Can and Cannot Contribute to Ethics: Francisco J. Ayala (University of California-Irvine) Part X: Is There a Place for Intelligent Design in the Philosophy of Biology? Introduction References and Further Reading 19. There Is a Place for Intelligent Design in the Philosophy of Biology: Intelligent Design in (Philosophy of) Biology: Some Legitimate Roles: Del Ratzsch (University of Massachusetts-Amherst) 20. There Is No Place for Intelligent Design in the Philosophy of Biology: Intelligent Design Is Not Science: Francisco J. Ayala (University of California-Irvine) Index

Contemporary Debates in Philosophy of Biology

Acknowledgments: The Oscar Speech George Clooney Never Got to Make. Introduction: Riddle Me This... Part One: Does the Dark Knight Always Do Right? 1. Why Doesn't Batman Kill the Joker (Mark D. White)? 2. Is It Right to Make a Robin (James DiGiovanna)? 3. Batman's Virtuous Hatred (Stephen Kershnar). Part Two: Law, Justice, and the Social Order: Where Does Batman Fit In? 4. No Man's Land: Social Order in Gotham City and New Orleans (Brett Chandler Patterson). 5. Governing Gotham (Tony Spanakos). 6. The Joker's Wild: Can We Hold the Clown Prince Morally Responsible (Christopher Robichaud). Part Three: Origins and Ethics: Becoming The Caped Crusader. 7. Batman's Promise (Randall M. Jensen). 8. Should Bruce Wayne Have Become Batman (Mahesh Ananth and Ben Dixon)? 9. What Would Batman Do? Bruce Wayne as Moral Exemplar (Ryan Indy Rhodes and David Kyle Johnson). Part Four: Who is the Batman? (Is That a Trick Question?) 10. Under the mask: How Any Person Can Become Batman (Sarah KI. Donovan and Nicholas P. Richardson). 11. Could Batman Have Been the Joker (Sam Cowling and Chris Ragg)? 12. Batman's Identity Crisis and Wittgenstein's Family Resemblance (Jason Southworth). 13. What Is It Like to Be a Batman (Ron Novy)? Part Five: Being The Vat: Insights From Existentialism and Taoism. 14. Alfred, the Dark Knight of Faith: Batman and Kierkegaard (Christopher M. Drohan). 15. Dark Nights and the Call of conscience (Jason J. Howard). 16. Batman's Confrontation with Death, Angst, and Freedom (David M. Hart). Part Six: Friend,Father... Rival? The Many Roles of the Bat. 17. Why Batman IS Better than Superman (Galen Foresman). 18. World's Finest...Friends? Batman, Superman, and the Nature of Friendship (Daniel P. Malloy). 19. Leaving the Shadow of the Bat: Aristotle, Kant, and Dick Grayson on Moral Education (Carsten Fogh Nielsen). 20. The Tao of the Bat (Bat-Tzu). Contributors. Index.

Batman and Philosophy: The Dark Knight of the Soul

An account of how humans evolved a conscious, vision-related ability unique to their species in order to solve nonroutine problems. In order to solve problems, humans are able to synthesize apparently unrelated concepts, take advantage of serendipitous opportunities, hypothesize, invent, and engage in other similarly abstract and creative activities, primarily through the use of their visual systems. In Scenario Visualization, Robert Arp offers an evolutionary account of the unique human ability to solve nonroutine vision-related problems. He argues that by the close of the Pleistocene epoch, humans evolved a conscious creative problem-solving capacity, which he terms scenario visualization, that enabled them to outlive other hominid species and populate the planet. Arp shows that the evidence for scenario visualization-by which images are selected, integrated, and then transformed and projected into visual scenarios-can be found in the kinds of complex tools our hominid ancestors invented in order to survive in the ever-changing environments of the Pleistocene world. Arp also argues that this conscious capacity shares an analogous affinity with neurobiological processes of selectivity and integration in the visual system, and that similar processes can be found in the activities of organisms in general. The evolution of these processes, he writes, helps account for the modern-day conscious ability of humans to use visual information to solve nonroutine problems creatively in their environments. Arp's account of scenario visualization and its emergence in evolutionary history suggests an answer to two basic questions asked by philosophers and biologists concerning human nature: why we are unique; and how we got that way. Robert Arp is Postdoctoral Research Fellow at the National Center for Biomedical Ontology. His areas of specialization include philosophy of biology and philosophy of mind. He is the author of numerous articles and the forthcoming An Integrated Approach to the Philosophy of Mind.

Robert Arp

Papers

Building Ontologies with Basic Formal Ontology

Function, Role and Disposition in Basic Formal Ontology

Contemporary Debates in Philosophy of Biology

Batman and Philosophy: The Dark Knight of the Soul

Scenario Visualization: An Evolutionary Account of Creative Problem Solving