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Philosophy of Biology

Edited by John Wilkins (University of Sydney, University of Melbourne)
Assistant editor: Justin Bzovy (University of Western Ontario)
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  1. added 2014-12-21
    Mark A. Musen, Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne Story & Barry Smith (2012). The National Center for Biomedical Ontology. Journal of the American Medical Informatics Association 19 (2):190-195.
    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...)
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  2. added 2014-12-21
    Daniel L. Rubin, Noy N. F. and Musen M. A. Lewis, Chris J. Mungall, Sima Misra, Monty Westerfield, Michael Ashburner, Ida Sim, Christopher G. Chute, Harold Solbrig, Margaret A. Storey, Barry Smith, John D. Richter, Natasha F. Noy & Mark A. Musen (2006). The National Center for Biomedical Ontology: Advancing Biomedicine Through Structured Organization of Scientific Knowledge. Omics: A Journal of Integrative Biology, 10(2), 2006, 10 (2):185-198.
    The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...)
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  3. added 2014-12-20
    Daniel Shargel (forthcoming). Emotions Without Objects. Biology and Philosophy:1-14.
    It is widely assumed that emotions have particular intentional objects. This assumption is consistent with the way that we talk: when we attribute states of anger, we often attribute anger at someone, or at something. It is also consistent with leading theories of emotion among philosophers and psychologists, according to which emotions are like judgments or appraisals. However, there is evidence from the social psychology literature suggesting that this assumption is actually false. I will begin by presenting a criterion for (...)
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  4. added 2014-12-20
    Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu (2011). The Protein Ontology: A Structured Representation of Protein Forms and Complexes. Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...)
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  5. added 2014-12-18
    Jonathan Birch & Samir Okasha (forthcoming). Kin Selection and Its Critics. BioScience.
    Hamilton’s theory of kin selection is the best-known framework for understanding the evolution of social behavior but has long been a source of controversy in evolutionary biology. A recent critique of the theory by Nowak, Tarnita, and Wilson sparked a new round of debate, which shows no signs of abating. In this overview, we highlight a number of conceptual issues that lie at the heart of the current debate. We begin by emphasizing that there are various alternative formulations of Hamilton’s (...)
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  6. added 2014-12-17
    Lindell Bromham (forthcoming). What is a Gene For? Biology and Philosophy:1-21.
    The word “gene” means different things to different people, and can even be used in multiple ways by the same individual. In this review, I follow a particular thread running through Griffith and Stotz’s “Genetics and Philosophy: an introduction”, which is the way that methods of investigation influence the way we define the concept of “gene”, from nineteen century breeding experiments to twenty-first century big data bioinformatics. These different views lead to a set of gene concepts, which only partially overlap (...)
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  7. added 2014-12-17
    Lucas J. Mix (2014). Proper Activity, Preference, and the Meaning of Life. Philosophy and Theory in Biology 6.
    The primary challenge for generating a useful scientific definition of life comes from competing concepts of biological activity and our failure to make them explicit in our models. I set forth a three-part scheme for characterizing definitions of life, identifying a binary , a range , and a preference . The three components together form a proper activity in biology . To be clear, I am not proposing that proper activity be adopted as the best definition of life or even (...)
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  8. added 2014-12-17
    Andreas Dorschel (1990). Der Mensch als Tier. Anmerkungen zum Programm der ‘human sociobiology’. Prima Philosophia 3 (2).
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  9. added 2014-12-17
    Andreas Dorschel (1990). Die soziobiologische Obsoletierung des ‘Reichs der Zwecke’. Zum Versuch der naturwissenschaftlichen Legitimation einer zynischen Anthropologie. Gregorianum 71 (1):5-22.
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  10. added 2014-12-17
    Andreas Dorschel (1990). Kulturevolution, Biologie und Sprache. Empirische und rationale Selektionskriterien. Deutsche Zeitschrift für Philosophie 38 (10):984-992.
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  11. added 2014-12-16
    Brian Key (forthcoming). Fish Do Not Feel Pain and its Implications for Understanding Phenomenal Consciousness. Biology and Philosophy:1-17.
    Phenomenal consciousness or the subjective experience of feeling sensory stimuli is fundamental to human existence. Because of the ubiquity of their subjective experiences, humans seem to readily accept the anthropomorphic extension of these mental states to other animals. Humans will typically extrapolate feelings of pain to animals if they respond physiologically and behaviourally to noxious stimuli. The alternative view that fish instead respond to noxious stimuli reflexly and with a limited behavioural repertoire is defended within the context of our current (...)
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  12. added 2014-12-15
    Adrian Currie (forthcoming). Marsupial Lions and Methodological Omnivory: Function, Success and Reconstruction in Paleobiology. Biology and Philosophy:1-23.
    Historical scientists frequently face incomplete data, and lack direct experimental access to their targets. This has led some philosophers and scientists to be pessimistic about the epistemic potential of the historical sciences. And yet, historical science often produces plausible, sophisticated hypotheses. I explain this capacity to generate knowledge in the face of apparent evidential scarcity by examining recent work on Thylacoleo carnifex, the ‘marsupial lion’. Here, we see two important methodological features. First, historical scientists are methodological omnivores, that is, they (...)
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  13. added 2014-12-09
    Charbel N. El-Hani, Ana Maria R. de Alameida, Gilberto C. Bomfim, Leyla M. Joaquim, João Carlos M. Magalhães, Lia M. N. Meyer, Maiana A. Pitombo & Vanessa C. dos Santos (2014). The Contribution of History and Philosophy to the Problem of Hybrid Views About Genes in Genetics Teaching. In Michael R. Matthews (ed.), International Handbook of Research in History, Philosophy and Science Teaching. Springer. 469-520.
    Currently there are persistent doubts about the meaning and contributions of the gene concept, mostly related to its interpretation as a stretch of DNA encoding a single functional product, i.e., the classical molecular gene concept. There is, however, much conceptual variation around genes, leading to important difficulties in genetics teaching. We investigated whether and how conceptual variation related to the gene concept and gene function models is present in school science and what potential problems it may bring to genetics teaching (...)
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  14. added 2014-12-09
    Ross H. Nehm & Kostas Kampourakis (2014). History and Philosophy of Science and the Teaching of Macroevolution. In Michael R. Matthews (ed.), International Handbook of Research in History, Philosophy and Science Teaching. Springer. 401-421.
    Although macroevolution has been the subject of sustained attention in the history and philosophy of science (HPS) community, only in recent years have science educators begun to more fully engage with the topic. This chapter first explores how science educators have conceptualized macroevolution and how their perspectives align with the views from HPS. Second, it illustrates how science educators’ limited engagement with HPS scholarship on macroevolution has influenced construct delineation, measurement instrument development, and educational arguments about which aspects of macroevolution (...)
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  15. added 2014-12-09
    Kostas Kampourakis & Ross H. Nehm (2014). History and Philosophy of Science and the Teaching of Evolution: Students’ Conceptions and Explanations. In Michael R. Matthews (ed.), International Handbook of Research in History, Philosophy and Science Teaching. Springer. 377-399.
    A large body of work in science education indicates that evolution is one of the least understood and accepted scientific theories. Although scholarship from the history and philosophy of science (HPS) has shed light on many conceptual and pedagogical issues in evolution education, HPS-informed studies of evolution education are also characterized by conceptual weaknesses. In this chapter, we critically review such studies and find that some work lacks historically accurate characterizations of student ideas (preconceptions and misconceptions). In addition, although several (...)
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  16. added 2014-12-05
    Ingo Brigandt & Alan C. Love (2012). Conceptualizing Evolutionary Novelty: Moving Beyond Definitional Debates. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 318:417-427.
    According to many biologists, explaining the evolution of morphological novelty and behavioral innovation are central endeavors in contemporary evolutionary biology. These endeavors are inherently multidisciplinary but also have involved a high degree of controversy. One key source of controversy is the definitional diversity associated with the concept of evolutionary novelty, which can lead to contradictory claims (a novel trait according to one definition is not a novel trait according to another). We argue that this diversity should be interpreted in light (...)
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  17. added 2014-12-05
    Ingo Brigandt, Essay: Homology. The Embryo Project Encyclopedia.
    Homology is a central concept of comparative and evolutionary biology, referring to the presence of the same bodily parts (e.g., morphological structures) in different species. The existence of homologies is explained by common ancestry, and according to modern definitions of homology, two structures in different species are homologous if they are derived from the same structure in the common ancestor. Homology has traditionally been contrasted with analogy, the presence of similar traits in different species not necessarily due to common ancestry (...)
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  18. added 2014-12-02
    Brent D. Mishler (1999). Getting Rid of Species? In Robert A. Wilson (ed.), Species: New Interdisciplinary Essays. MIT Press. 307-315.
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  19. added 2014-12-02
    Kevin de Queiroz & Michael J. Donoghue (1990). Phylogenetic Systematics and Species Revisited. Cladistics 6 (1):83-90.
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  20. added 2014-11-28
    Klaus Gilgenmann & Bertold Schweitzer (2006). Homo – sociologicus – sapiens: Zur evolutionstheoretischen Einbettung soziologischer Menschenmodelle. Zeitschrift für Soziologie 35 (5):348–371.
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  21. added 2014-11-28
    Bertold Schweitzer & Klaus Gilgenmann (2005). Strukturelle Analogien bei biotischer und soziokultureller Evolution. Erwägen Wissen Ethik 16 (3):421–424.
    The article by B. Stephan (this issue) describes characteristics and stages of change of sociobiological and socio-cultural units. However, neither analogy nor evolutionary and developmental concept are sufficiently precise. In addition, Stephan pays no attention to structural analogies between biotic and cultural change, and therefore comes to the misguided assessment that socio-cultural change is to be construed as a developmental rather than an evolutionary process.
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  22. added 2014-11-26
    Thomas Pradeu (forthcoming). Toolbox Murders: Putting Genes in Their Epigenetic and Ecological Contexts: A Review of Griffiths and Stotz, Genetics and Philosophy: An Introduction. [REVIEW] Biology and Philosophy.
    Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what (...)
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  23. added 2014-11-26
    Maureen O'Malley, Ingo Brigandt, Alan C. Love, John W. Crawford, Jack A. Gilbert, Rob Knight, Sandra D. Mitchell & Forest Rohwer (2014). Multilevel Research Strategies and Biological Systems. Philosophy of Science 81:811-828.
    Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.
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  24. added 2014-11-24
    Heather Dyke & James Maclaurin (2013). Evolutionary Explanations of Temporal Experience. In Heather Dyke & Adrian Bardon (eds.), A Companion to the Philosophy of Time. Wiley-Blackwell. 521-535.
    A common approach in the Philosophy of Time, particularly in enquiry into the metaphysical nature of time, has been to examine various aspects of the nature of human temporal experience, and ask what, if anything, can be discerned from this about the nature of time itself. Many human traits have explanations that reside in facts about our evolutionary history. We ask whether features of human temporal experience might admit of such evolutionary explanations. We then consider the implications of any proposed (...)
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  25. added 2014-11-23
    Trevor Pearce (2014). The Dialectical Biologist, Circa 1890: John Dewey and the Oxford Hegelians. Journal of the History of Philosophy 52 (4):747-777.
    I argue in this paper that rather than viewing John Dewey as either a historicist (inspired by Hegel) or a naturalist (inspired by biology), we should see him as strange but potentially fruitful combination of both. I will demonstrate that the notion of organism-environment interaction central to Dewey’s pragmatism stems from a Hegelian approach to adaptation; his turn to biology was not necessarily a turn away from Hegel. I argue that Dewey’s account of the organism-environment relation derives from the work (...)
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  26. added 2014-11-19
    Duncan Purves (2014). Anthropocentric Indirect Arguments and Anthropocentric Moral Attitudes. Ethics, Policy and Environment 17 (3):267-270.
    Anthropocentric indirect arguments , which call for specific policies or actions because of human benefits that are correlated with but not caused by benefits to the environment, are gaining increasing traction with those who take a pragmatic approach to environmental protection. I contend that nonanthropocentrists might remain justifiably uneasy about AIAs because such arguments fail to challenge prevailing speciesist moral attitudes. I close by considering whether Elliott can address this concern of nonanthropocentrists by appealing to the ability of AIAs to (...)
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  27. added 2014-11-19
    Laura Smith (2014). On the ‘Emotionality’ of Environmental Restoration: Narratives of Guilt, Restitution, Redemption and Hope. Ethics, Policy and Environment 17 (3):286-307.
    This paper presents a moral–emotional critique of environmental restoration, through discussion of narratives of redemption. The importance of ‘redemption’ vis-à-vis other environmental discourses rests with its capacity to unpack how, why and in what circumstances the idea of ‘putting something back’ for nature exerts a hold on the popular imagination. This paper thus examines the ethical and emotional experiences bound up in restoration discourses, to identify the motives deployed to confront shame and an associated guilt, and achieve restitution. In turn, (...)
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  28. added 2014-11-19
    Kevin C. Elliott (2014). Anthropocentric Indirect Arguments for Environmental Protection. Ethics, Policy and Environment 17 (3):243-260.
    Environmental ethicists have devoted considerable attention to discussing whether anthropocentric or nonanthropocentric arguments provide more appropriate means for defending environmental protection. This paper argues that philosophers, scientists, and policy makers should pay more attention to a particular type of anthropocentric argument. These anthropocentric indirect arguments defend actions or policies that benefit the environment, but they justify the policies based on beneficial effects on humans that are not caused by their environmental benefits. AIAs appear to have numerous appealing characteristics, and their (...)
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  29. added 2014-11-19
    Jeremy Bendik-Keymer (2014). Living Up to Our Humanity: The Elevated Extinction Rate Event and What It Says About Us. Ethics, Policy and Environment 17 (3):339-354.
    Either we are in an elevated extinction rate event or in a mass extinction. Scientists disagree, and the matter cannot be resolved empirically until it is too late. We are the cause of the elevated extinction rate. What does this say about us, we who are Homo sapiens—the wise hominid? Beginning with the Renaissance and spreading during the 18th century, the normative notion of humanity has arisen to stand for what expresses our dignity as humans—specifically our thoughtfulness, in the double (...)
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  30. added 2014-11-19
    Thomas Heyd (2014). Symbolically Laden Sites in the Landscape and Climate Change. Ethics, Policy and Environment 17 (3):355-369.
    Attention is drawn to the threat posed by climate change to symbolically laden places, landscapes and landmarks, and suggested that, insofar as some of those sites are treated as sacred by certain populations, their disturbance may be especially problematic. Special consideration is given to the significance glacial retreat for local, nearby populations, and its importance from the point of view of climate justice and ethics is discussed. The potential value of iconic sites from the perspective of engagement and action on (...)
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  31. added 2014-11-19
    David Storey (2014). ‘Anthropocentric Indirect Arguments for Environmental Protection,’ Kevin Elliott; Anthropocentric Indirect Arguments: A Risky Business? Ethics, Policy and Environment 17 (3):279-282.
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  32. added 2014-11-19
    Jennifer Mcerlean (2014). The Accidental Environmentalist: Elliott on Anthropocentric Indirect Arguments. Ethics, Policy and Environment 17 (3):283-285.
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  33. added 2014-11-19
    Francesca Pongiglione (2014). Motivation for Adopting Pro-Environmental Behaviors: The Role of Social Context. Ethics, Policy and Environment 17 (3):308-323.
    This article investigates the origin of the lack of motivation for adopting significant pro-environmental behavior . I identify three main barriers to motivation: the feeling that there is a need for broad collective action that has not yet materialized, the lack of practical knowledge about what an individual can do in his/her daily life to address environmental problems, and insufficient feedback and approval mechanisms. Subsequently, I argue that an individual's social context may contribute in addressing all three. The motivation for (...)
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  34. added 2014-11-19
    Dan C. Shahar (2014). Integrity Versus Expediency for Non-Anthropocentrists. Ethics, Policy and Environment 17 (3):271-274.
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  35. added 2014-11-19
    Greg Bothun (2014). Do Anthropocentric Indirect Arguments Have Any Scientific Validity? A Commentary on Anthropocentric Indirect Arguments for Environmental Protection, by K. Elliot. Ethics, Policy and Environment 17 (3):275-278.
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  36. added 2014-11-19
    Eric Katz (2014). Anthropocentric Indirect Arguments: Return of the Plastic-Tree Zombies. Ethics, Policy and Environment 17 (3):264-266.
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  37. added 2014-11-19
    David R. Morrow (2014). Earthmasters: The Dawn of the Age of Climate Engineering/A Case for Climate Engineering. Ethics, Policy and Environment 17 (3):370-373.
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  38. added 2014-11-19
    Sarah E. Fredericks (2014). Ethics in Agenda 21. Ethics, Policy and Environment 17 (3):324-338.
    Although environmental ethicists often focus on applying ethics to policy, the ethics embedded in policy documents such as Agenda 21 are also significant. Though largely ignored by ethicists after early responses to the document focused on intrinsic value, Agenda 21's ethics are particularly valuable for their ability to resonate with many people and link politics, technical studies, and ethics. For instance, their use draws attention to the need to ethically evaluate sustainability indexes and identifies limitations of existing indexes. At a (...)
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  39. added 2014-11-19
    Chad J. McGuire (2014). Losing the Message: Some Policy Implications of Anthropocentric Indirect Arguments for Environmental Protection. Ethics, Policy and Environment 17 (3):261-263.
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  40. added 2014-11-17
    Esteban Hasson (ed.) (2012). Darwin En El Sur, Ayer y Hoy: Contribuciones de la 1ra. Reunión de Biología Evolutiva Del Cono Sur. Libros Del Rojas, Universidad de Buenos Aires.
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  41. added 2014-11-15
    David Ludwig (forthcoming). Indigenous and Scientific Kinds. British Journal for the Philosophy of Science.
    The aim of this article is to discuss the relation between indigenous and scientific kinds on the basis of contemporary ethnobiological research. I argue that ethnobiological accounts of taxonomic convergence-divergence patters challenge common philosophical models of the relation between folk concepts and natural kinds. Furthermore, I outline a positive model of taxonomic convergence-divergence patterns that is based on Slater's [2014] notion of “stable property clusters” and Franklin-Hall's [2014] discussion of natural kinds as “categorical bottlenecks.” Finally, I argue that this model (...)
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  42. added 2014-11-11
    Geoffrey K. Chambers (forthcoming). Understanding Complexity: Are We Making Progress? Biology and Philosophy:1-10.
    In recent years a new conceptual tool called Complexity Theory has come to the attention of scientists and philosophers. This approach is concerned with the emergent properties of interacting systems. It has found wide applicability from cosmology to Social Structure Analysis. However, practitioners are still struggling to find the best way to define complexity and then to measure it. A new book Complexity and the arrow of time by Lineweaver et al. contains contributions from scholars who provide critical reviews of (...)
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  43. added 2014-11-11
    Thomas Ferenci & Ram Maharjan (forthcoming). Mutational Heterogeneity: A Key Ingredient of Bet-Hedging and Evolutionary Divergence? Bioessays:n/a-n/a.
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  44. added 2014-11-11
    David Hull (1999). On the Plurality of Species: Questioning the Party Line. In R. Wilson (ed.), Species: New Interdisciplinary Essays. MIT Press. 23-48.
  45. added 2014-11-11
    Ernst Mayr & Peter D. Ashlock (1991). Principles of Systematic Zoology. McGraw-Hill.
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  46. added 2014-11-11
    Ernst Mayr (1970). Populations, Species and Evolution: An Abridgment of Animal Species and Evolution. Belknap Press of Harvard University Press.
    In the Preface of Animal Species and Evolution (1963), I wrote that it was "an attempt to summarize and review critically what we know about the biology and genetics of animal species and their role in evolution." The result was a volume of XIV ...
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  47. added 2014-11-11
    Ernst Mayr (1963). Animal Species and Evolution. Belknap of Harvard University Press.
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  48. added 2014-11-11
    Ernst Mayr (1942). Systematics and the Origin of Species From the Viewpoint of a Zoologist. Columbia University Press.
    WE HAVE LEARNED in the preceding chapter that a revolutionary change of the species concept is in the making, a change which not only affects taxonomic procedure, but which also contributes considerably toward a better understanding of ...
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  49. added 2014-11-09
    Emanuele Serrelli, The Extended Evolutionary Synthesis: A Metascientific View of Evolutionary Biology, and Some Directions to Transcend its Limits.
    To approach the issue of the recent proposal of an Extended Evolutionary Synthesis (EES) put forth by Massimo Pigliucci and Gerd Müller, I suggest to consider the EES as a metascientific view: a description of what’s new in how evolutionary biology is carried out, not only a description of recently learned aspects of evolution. Knowing ‘what is it to do research’ in evolutionary biology, today versus yesterday, can aid training, research and career choices, establishment of relationships and collaborations, decision of (...)
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  50. added 2014-11-07
    Brendan Mahoney (2014). Heidegger and the Art of Technology. Environmental Philosophy 11 (2):279-306.
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