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  1. Francisco J. Ayala, The Structure of Evolutionary Theory: On Stephen Jay Gould's Monumental Masterpiece.
    Stephen Jay Gould’s monumental The Structure of Evolutionary Theory ‘‘attempts to expand and alter the premises of Darwinism, in order to build an enlarged and distinctive evolutionary theory . . . while remaining within the tradition, and under the logic, of Darwinian argument.’’ The three branches or ‘‘fundamental principles of Darwinian logic’’ are, according to Gould: agency (natural selection acting on individual organisms), efficacy (producing new species adapted to their environments), and scope (accumulation of changes that through geological time yield (...)
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  2. Francisco J. Ayala (2010). Darwin and Intelligent Design. In Science and Religion in Dialogue. Wiley-Blackwell. 749-766.
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  3. Francisco J. Ayala (2010). Science and Religion in Dialogue. Wiley-Blackwell.
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  4. Francisco J. Ayala (2010). The Biological Foundations of Ethics. Revista Portuguesa de Filosofia 66 (3):523 - 537.
    Erect posture and large brain are two of the most significant anatomical traits that distinguish us from nonhuman primates. But humans are also different from chimpanzees and other animals, and no less importantly, in their behavior, both as individuals and socially. Distinctive human behavioral attributes include tool-making and technology; abstract thinking, categorizing, and reasoning; symbolic (creative) language; self-awareness and death-awareness; science, literature, and art; legal codes, ethics and religion; complex social organization and political institutions. These traits may all be said (...)
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  5. Francisco J. Ayala (2010). There is No Place for Intelligent Design in the Philosophy of Biology : Intelligent Design is Not Science. In Francisco José Ayala & Robert Arp (eds.), Contemporary Debates in Philosophy of Biology. Wiley-Blackwell Pub.. 364--390.
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  6. Francisco José Ayala & Robert Arp (eds.) (2010). Contemporary Debates in Philosophy of Biology. Wiley-Blackwell Pub..
    This collection of specially commissioned essays puts top scholars head to head to debate the central issues in the lively and fast growing field of philosophy ...
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  7. Francisco J. Ayala (2009). Masters. Causality and Design : Teleological Explanations in the Living World. In González Recio & José Luis (eds.), Philosophical Essays on Physics and Biology. G. Olms.
     
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  8. Francisco J. Ayala (2008). Ensayo sobre las bases biológicas del comportamiento moral. Estudios Filosóficos 57 (165):225-246.
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  9. Francisco J. Ayala (2008). Icons of Evolution An Encyclopedia of People, Evidence, and Controversies.(2008). Editor Brian Regal. Greenwood Press. Hardback, 687 Pp. ISBN: 978‐0‐313‐33911‐0. [REVIEW] Bioessays 30 (11‐12):1252-1253.
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  10. Vladimir Cachón, Ana Barahona & Francisco J. Ayala (2008). The Rhetorical Construction of Eldredge and Gould's Article on the Theory of Punctuated Equilibria in 1972. History and Philosophy of the Life Sciences 30 (3/4):317 - 337.
    This article seeks to show how several rhetorical tools were used and, in fact, played a central role in the argumentation advanced by Niles Eldredge and Stephen Jay Gould in their 1972 seminal article on the theory of Punctuated Equilibria. It is analyzed how Eldredge and Gould proceeded through three steps that, sequentially integrated, made their argument compelling. It is shown how they made use of analogies, metaphors and other rhetorical tools. It is sustained that they began by priming the (...)
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  11. Francisco J. Ayala (2007). Human Evolution: The Three Grand Challenges of Human Biology. In David L. Hull & Michael Ruse (eds.), The Cambridge Companion to the Philosophy of Biology. Cambridge University Press.
     
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  12. Francisco J. Ayala (2007). The Vatican and Evolution. [REVIEW] History and Philosophy of the Life Sciences 29 (2):225 - 229.
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  13. John S. Wilkins, Walter M. Fitch & Francisco J. Ayala (2007). Systematics and the Origin of Species: On Ernst Mayr's 100th Anniversary. Biology and Philosophy 22 (4):603-610.
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  14. Francisco J. Ayala (2006). Evolution Vs. Creationism. [REVIEW] History and Philosophy of the Life Sciences 28 (1):71 - 82.
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  15. Francisco J. Ayala (2006). The Blasphemy of Intelligent Design. [REVIEW] History and Philosophy of the Life Sciences 28 (3):409 - 421.
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  16. Francisco J. Ayala (2006). The Politics of Science. Bioscience 56 (1):78.
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  17. Francisco J. Ayala (2005). Life: The Short(Er) Version. Bioscience 55 (9):801.
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  18. Ana Barahonas, Susana Pinar & Francisco J. Ayala (2005). Introduction and Institutionalization of Genetics in Mexico Ana Barahona, Susana Pinar and Francisco J. Ayala. Journal of the History of Biology 38 (2):273 - 299.
    We explore the distinctive characteristics of Mexico's society, politics and history that impacted the establishment of genetics in Mexico, as a new disciplinary field that began in the early 20th century and was consolidated and institutionalized in the second half. We identify about three stages in the institutionalization of genetics in Mexico. The first stage can be characterized by Edmundo Taboada, who was the leader of a research program initiated during the Cárdenas government (1934-1940), which was primarily directed towards improving (...)
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  19. Jessica L. Green, Alan Hastings, Peter Arzberger, Francisco J. Ayala, Kathryn L. Cottingham, Kim Cuddington, Frank Davis, Jennifer A. Dunne, Marie-josée Fortin, Leah Gerber & Michael Neubert (2005). Complexity in Ecology and Conservation: Mathematical, Statistical, and Computational Challenges. Bioscience 55 (6):501.
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  20. Francisco Rodríguez‐Trelles, Rosa Tarrío & Francisco J. Ayala (2005). Is Ectopic Expression Caused by Deregulatory Mutations or Due to Gene‐Regulation Leaks with Evolutionary Potential? Bioessays 27 (6):592-601.
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  21. Francisco J. Ayala (2003). Intelligent Design: The Original Version. Theology and Science 1 (1):9-32.
    William Paley ( Natural Theology , 1802) developed the argument-from-design. The complex structure of the human eye evinces that it was designed by an intelligent Creator. The argument is based on the irreducible complexity ("relation") of multiple interacting parts, all necessary for function. Paley adduces a wealth of biological examples leading to the same conclusion; his knowledge of the biology of his time was profound and extensive. Charles Darwin’s Origin of Species is an extended argument demonstrating that the "design" of (...)
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  22. Francisco J. Ayala (2000). An American Malaise: The Debate Between Darwin and Christian Fundamentalism. [REVIEW] History and Philosophy of the Life Sciences 22 (2):273 - 293.
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  23. Francisco J. Ayala (2000). Debating Darwin. Biology and Philosophy 15 (4):559-573.
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  24. Francisco J. Ayala (2000). Evolution of Biological Diversity. Bioessays 22 (7):681-682.
  25. Francisco José Ayala (2000). ¿ Desde África? Una perspectiva de los elementos poblacionales en la aparición de los seres humanos modernos. Ludus Vitalis 8 (13):135-156.
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  26. Francisco J. Ayala (1999). Adaptation and Novelty: Teleological Explanations in Evolutionary Biology. History and Philosophy of the Life Sciences 21 (1):3 - 33.
    Knives, birds' wings, and mountain slopes are used for certain purposes: cutting, flying, and climbing. A bird's wings have in common with knives that they have been 'designed' for the purpose they serve, which purpose accounts for their existence, whereas mountain slopes have come about by geological processes independently of their uses for climbing. A bird's wings differ from a knife in that they have not been designed or produced by any conscious agent; rather, the wings, like the slopes, are (...)
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  27. Francisco J. Ayala (1999). Molecular Clock Mirages. Bioessays 21 (1):71-75.
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  28. Francisco J. Ayala (1998). Biology Precedes, Culture Transcends: An Evolutionist's View of Human Nature. Zygon 33 (4):507-523.
  29. Francisco J. Ayala (1998). Teleological Explanations Versus Teleology. History and Philosophy of the Life Sciences 20 (1):41 - 50.
  30. Francisco J. Ayala (1997). Genetics and the Origin of Species: National Academy of Sciences Colloquium, Irvine, California, 30 January‐1 February, 1997. [REVIEW] Bioessays 19 (7):651-652.
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  31. Francisco J. Ayala (1995). Adam, Eve, and Other Ancestors: A Story of Human Origins Told by Genes. [REVIEW] History and Philosophy of the Life Sciences 17 (2):303 - 313.
  32. Francisco J. Ayala (1994). Las reglas del juego de la vida, o¿ existe progreso en la evolución biológica? Ludus Vitalis 2 (2):5-233.
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  33. Francisco J. Ayala (1994). On the Scientific Method, Its Practice and Pitfalls. History and Philosophy of the Life Sciences 16 (2):205 - 240.
    This paper sets forth a familiar theme, that science essentially consists of two interdependent episodes, one imaginative, the other critical. Hypotheses and other imaginative conjectures are the initial stage of scientific inquiry because they provide the incentive to seek the truth and a clue as to where to find it. But scientific conjectures must be subject to critical examination and empirical testing. There is a dialogue between the two episodes; observations made to test a hypothesis are the inspiration for new (...)
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  34. Michel Tibayrenc, Finn Kjellberg & Francisco J. Ayala (1991). The Clonal Theory of Parasitic Protozoa. Bioscience 41 (11):767-774.
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  35. Francisco J. Ayala (1989). Genetic Mixing. Bioscience 39 (1):45-46.
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  36. Francisco J. Ayala (1989). Genetic Mixing Origins of Sex: Three Billion Years of Genetic Recombination L. Margulis D. Sagan. Bioscience 39 (1):45-46.
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  37. Francisco J. Ayala (1989). Thermodynamics, Information, and Evolution: The Problem of Reductionism. [REVIEW] History and Philosophy of the Life Sciences 11 (1):115 - 120.
  38. Francisco J. Ayala (1988). Creation/Evolution Controversies Science and Earth History: The Evolution/Creation Controversy A. N. Strahler. Bioscience 38 (10):705-707.
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  39. Francisco J. Ayala (1988). Darwin and the Bible. [REVIEW] History and Philosophy of the Life Sciences 10 (1):137 - 144.
  40. Francisco J. Ayala (1988). The Nature of Scientific Discovery. [REVIEW] History and Philosophy of the Life Sciences 10 (1):129 - 136.
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  41. Francisco J. Ayala (1987). Sociobiology and Ethics. [REVIEW] History and Philosophy of the Life Sciences 9 (2):315 - 325.
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  42. Francisco J. Ayala (1987). The Biological Roots of Morality. Biology and Philosophy 2 (3):235-252.
    The question whether ethical behavior is biologically determined may refer either to thecapacity for ethics (e.i., the proclivity to judge human actions as either right or wrong), or to the moralnorms accepted by human beings for guiding their actions. My theses are: (1) that the capacity for ethics is a necessary attribute of human nature; and (2) that moral norms are products of cultural evolution, not of biological evolution.Humans exhibits ethical behavior by nature because their biological makeup determines the presence (...)
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  43. Francisco J. Ayala (1987). Understanding Extinction Animal Extinctions. What Everyone Should Know R. J. Hoage. Bioscience 37 (6):426-428.
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  44. Francisco J. Ayala (1986). The Theory of Evolution: The Case for Randomness in the Evolution of DNA and Proteins. [REVIEW] History and Philosophy of the Life Sciences 8 (1):129 - 138.
  45. Francisco J. Ayala (1985). Human Nature and Evolution. [REVIEW] History and Philosophy of the Life Sciences 7 (2):315 - 320.
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  46. Francisco J. Ayala (1985). Neo‐Darwinism: An Uneven Assessment. Evolutionary Theory: Paths Into the Future. Edited by J. W. POLLARD. John Wiley and Sons, 1984, Pp. 271. £21.50. [REVIEW] Bioessays 3 (1):44-45.
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  47. Francisco J. Ayala (1983). Entrevista Con Francisco J. Ayala. El Basilisco: Revista de Filosofía, Ciencias Humanas, Teoría de la Ciencia y de la Cultura 15:78-93.
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  48. Francisco J. Ayala (1982). A History of Evolutionary Theory The Evolutionary Synthesis: Perspectives in the Unification of Biology Ernst Mayr William B. Provine. Bioscience 32 (5):351-351.
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  49. Francisco J. Ayala (1982). Beyond Darwinism? The Challenge of Macroevolution to the Synthetic Theory of Evolution. PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1982:275 - 291.
    The theory of punctuated equilibrium has been proposed as a challenge to the modern synthesis of evolutionary theory. Two important issues are raised. The first is scientific: whether morphological change as observed in the paleontological record is essentially always associated with speciation events. This paper argues that there is at present no empirical support for this claim: the alleged evidence is based on a definitional fallacy. The second issue is epistemological: whether macroevolution is an autonomous field of study, independent from (...)
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  50. Francisco J. Ayala (1982). Readings in Evolutionary History Evolution: Genesis and Revelations with Readings From Empedocles to Wilson C. Leon Harris. Bioscience 32 (5):356-356.
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