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  1. Rachael L. Brown (2013). What Evolvability Really Is. British Journal for the Philosophy of Science (3):axt014.
    In recent years, the concept of evolvability has been gaining in prominence both within evolutionary developmental biology (evo-devo) and the broader field of evolutionary biology. Despite this, there remains considerable disagreement about what evolvability is. This article offers a solution to this problem. I argue that, in focusing too closely on the role played by evolvability as an explanandum in evo-devo, existing philosophical attempts to clarify the evolvability concept have been overly narrow. Within evolutionary biology more broadly, evolvability offers a (...)
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  2. A. Danchin (2014). The Logic of Metabolism and its Fuzzy Consequences. Environmental Microbiology 16 (1):19-28.
    Intermediary metabolism molecules are orchestrated into logical pathways stemming from history (L-amino acids, D-sugars) and dynamic constraints (hydrolysis of pyrophosphate or amide groups is the driving force of anabolism). Beside essential metabolites, numerous variants derive from programmed or accidental changes. Broken down, variants enter standard pathways, producing further variants. Macromolecule modification alters enzyme reactions specificity. Metabolism conform thermodynamic laws, precluding strict accuracy. Hence, for each regular pathway, a wealth of variants inputs and produces metabolites that are similar to but not (...)
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  3. Ferdinand Fellmann (2013). Emotional Selection and Human Personality. Biological Theory 8 (1):64-73.
    This article addresses the emergence of human personality in evolution. The mechanisms of natural and sexual selection developed by Darwin are not sufficient to explain the sense of self. Therefore we attempt to trace the evolutionary process back to a form of selection termed “emotional selection.” This involves reconstructing selection out of subjective qualities and showing how emotions enable human forms of life that are relevant for the cultural level of cooperation that marks our species. We see a paradigm shift (...)
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  4. Philippe Gagnon (2013). An Improbable God Between Simplicity and Complexity: Thinking About Dawkins's Challenge. International Philosophical Quarterly 53 (4):409-433.
    Richard Dawkins has popularized an argument that he thinks sound for showing that there is almost certainly no God. It rests on the assumptions (1) that complex and statistically improbable things are more difficult to explain than those that are not and (2) that an explanatory mechanism must show how this complexity can be built up from simpler means. But what justifies claims about the designer’s own complexity? One comes to a different understanding of order and of simplicity when one (...)
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  5. Justin Garson (2015). Carl F. Craver and Lindley Darden. In Search of Mechanisms: Discoveries Across the Life Sciences. [REVIEW] Hopos: The Journal of the International Society for the History of Philosophy of Science 5 (1):180-83.
    Carl F. Craver and Lindley Darden’s new book, In Search of Mechanisms: Discoveries across the Life Sciences, is a fantastic and lucid introduction to the “new mechanism” tradition in the philosophy of science. Over the last 2 decades, but particularly since the turn of the century, this has become an influential framework for thinking about core problems in the history and philosophy of science, with a strong emphasis on biology. There are at least four major aims. First, the new mechanism (...)
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  6. James Goetz (2006). The Extravagant Creator of Junk DNA. International Society for Complexity, Information, and Design Archive.
    Denton proposes a hypothesis of frontloaded teleological evolution while Denton suggests that a vast amount of junk DNA is incompatible with his model of teleology and perhaps any model of teleology. This paper outlines a hypothesis for a vast amount of junk DNA with no selective constraints, and proposes that the junk DNA is compatible with teleological evolution that included occasional intervention during the history of adaptive evolution. And this paper introduces a hypothesis for the necessity of intervention in the (...)
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  7. Stavros Ioannidis (2013). Regulatory Evolution and Theoretical Arguments in Evolutionary Biology. Science and Education 22 (2):279-292.
    The cis-regulatory hypothesis is one of the most important claims of evolutionary developmental biology. In this paper I examine the theoretical argument for cis-regulatory evolution and its role within evolutionary theorizing. I show that, although the argument has some weaknesses, it acts as a useful example for the importance of current scientific debates for science education.
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  8. Marvin E. Kirsh (2011). Evolution At the Surface of Euclid:Elements of A Long Infinity in Motion Along Space. International Journal of the Arts and Sciences 4 (2):71-96.
    It is modernly debated whether application of the free will has potential to cause harm to nature. Power possessed to the discourse, sensory/perceptual, physical influences on life experience by the slow moving machinery of change is a viral element in the problems of civilization; failed resolution of historical paradox involving mind and matter is a recurring source of problems. Reference is taken from the writing of Euclid in which a oneness of nature as an indivisible point of thought is made (...)
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  9. Hugh LaFollette & Niall Shanks (1994). Animal Experimentation: The Legacy of Claude Bernard. International Studies in the Philosophy of Science 8 (3):195 – 210.
    Claude Bernard, the father of scientific physiology, believed that if medicine was to become truly scientiifc, it would have to be based on rigorous and controlled animal experiments. Bernard instituted a paradigm which has shaped physiological practice for most of the twentieth century. ln this paper we examine how Bernards commitment to hypothetico-deductivism and determinism led to (a) his rejection of the theory of evolution; (b) his minima/ization of the role of clinical medicine and epidemiological studies; and (c) his conclusion (...)
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  10. Ehud Lamm (2010). Review Of: Julian Huxley, Evolution: The Modern Synthesis – The Definitive Edition. [REVIEW] Integrative Psychological and Behavioral Science.
    The review focuses on Huxley’s debt to Richard Goldschmidt and Cyril Darlington. I discuss the conceptions of the genome developed by Goldschmidt and Darlington and their continuing relevance.
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  11. Ehud Lamm & Ohad Kammar (forthcoming). Inferring Co-Evolution. Philosophy of Science.
    We discuss two inference patterns for inferring the coevolution of two characters based on their properties at a single point in time and determine when developmental interactions can be used to deduce evolutionary order. We discuss the use of the inference patterns we present in the biological literature and assess the arguments’ validity, the degree of support they give to the evolutionary conclusion, how they can be corroborated with empirical evidence, and to what extent they suggest new empirically addressable questions. (...)
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  12. John Matthewson & Brett Calcott, Mechanistic Explanation Without Mechanisms.
    We provide an account of mechanistic representation and explanation that has several advantages over previous proposals. In our view, explaining mechanistically is not simply giving an explanation of a mechanism. Rather, an explanation is mechanistic because of particular relations that hold between a mechanical representation, or model, and the target of explanation. Under this interpretation, mechanistic explanation is possible even when the explanatory target is not a mechanism. We argue that taking this view is not only coherent and plausible, it (...)
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  13. Nicholas Maxwell (2010). Darwinian Theory Reinterpreted. In N. Maxwell (ed.), Cutting God in Half - And Putting the Pieces Together Again: A New Approach to Philosophy. Pentire Press. 264-300.
    It is argued that purposive action of living things plays a crucial role in Darwinian evolution. As evolution proceeds, the mechanisms of evolution evolve as well, giving an increasingly important role to purposive action - to be understood in a sense which is compatible with physics (the atom of purposiveness being the thermostat). Nine versions of Darwinian theory are distinguished. The first denies that purposive action has any role in evolution at all; each successive version gives an inceasingly important role (...)
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  14. Erika Milam, Roberta L. Millstein, Angela Potochnik & Joan Roughgarden (2011). Sex and Sensibility: The Role of Social Selection. Metascience 20 (2):253-277.
    Sex and sensibility: The role of social selection Content Type Journal Article DOI 10.1007/s11016-010-9464-6 Authors Erika L. Milam, Department of History, University of Maryland, 2115 Francis Scott Key Hall, College Park, MD 20742, USA Roberta L. Millstein, Department of Philosophy, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA Angela Potochnik, Department of Philosophy, University of Cincinnati, P.O. Box 210374, Cincinnati, OH 45221, USA Joan E. Roughgarden, Department of Biology, Stanford University, Stanford, CA 94305-5020, USA Journal Metascience Online (...)
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  15. Roberta L. Millstein (2012). Darwin's Explanation of Races by Means of Sexual Selection. Studies in History and Philosophy of Biological and Biomedical Sciences 43 (3):627-633.
    In Darwin’s Sacred Cause, Adrian Desmond and James Moore contend that ‘‘Darwin would put his utmost into sexual selection because the subject intrigued him, no doubt, but also for a deeper reason: the theory vindicated his lifelong commitment to human brotherhood’’ (2009: p. 360). Without questioning Des- mond and Moore’s evidence, I will raise some puzzles for their view. I will show that attention to the structure of Darwin’s arguments in the Descent of Man shows that they are far from (...)
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  16. Roberta L. Millstein (2000). Chance and Macroevolution. Philosophy of Science 67 (4):603-624.
    When philosophers of physics explore the nature of chance, they usually look to quantum mechanics. When philosophers of biology explore the nature of chance, they usually look to microevolutionary phenomena, such as mutation or random drift. What has been largely overlooked is the role of chance in macroevolution. The stochastic models of paleobiology employ conceptions of chance that are similar to those at the microevolutionary level, yet different from the conceptions of chance often associated with quantum mechanics and Laplacean determinism.
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  17. Marcin Miłkowski (2009). Is Evolution Algorithmic? Minds and Machines 19 (4):465-475.
    In Darwin’s Dangerous Idea, Daniel Dennett claims that evolution is algorithmic. On Dennett’s analysis, evolutionary processes are trivially algorithmic because he assumes that all natural processes are algorithmic. I will argue that there are more robust ways to understand algorithmic processes that make the claim that evolution is algorithmic empirical and not conceptual. While laws of nature can be seen as compression algorithms of information about the world, it does not follow logically that they are implemented as algorithms by physical (...)
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  18. H. Allen Orr (2005). Theories of Adaptation: What They Do and Don’T Say. Genetics.
    Theoretical work on adaptation has lagged behind experimental. But two classes of adaptation model have been partly explored. One is phenotypic and the other DNA sequence based. I briefly consider an example of each – Fisher’s geometric model and Gillespie’s mutational landscape model, respectively – reviewing recent results. Despite their fundamental differences, these models give rise to several strikingly similar
    results. I consider possible reasons for this congruence. I also emphasize what predictions do and, as important, do not follow from these (...)
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  19. Massimo Pigliucci (2012). Philosophical Reflections on Darwin and Evolutionary Theory. [REVIEW] Trends in Ecology and Evolution 27 (5):258.
    Few scientists are conscious of the distinc- tion between the logic of what they write and the rhetoric of how they write it. This is because we are taught to write scientific papers and books from a third-person per- spective, using as impersonal (and, almost inevitably, boring [1]) a style as possible. The first chapter in Elliott Sober’s new book examines the difference between Darwin’s logic and his rhetoric in The Origin, and manages to teach some interesting and in- sightful (...)
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  20. Massimo Pigliucci (2012). Landscapes, Surfaces, and Morphospaces: What Are They Good For? In E. Svensson & R. Calsbeek (eds.), The Adaptive Landscape in Evolutionary Biology.
    Few metaphors in biology are more enduring than the idea of Adaptive Landscapes, originally proposed by Sewall Wright (1932) as a way to visually present to an audience of typically non- mathematically savvy biologists his ideas about the relative role of natural selection and genetic drift in the course of evolution. The metaphor, how- ever, was born troubled, not the least reason for which is the fact that Wright presented different diagrams in his original paper that simply can- not refer (...)
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  21. Massimo Pigliucci (2007). Do We Need an Extended Evolutionary Synthesis? Evolution 61 (12):2743-2749.
    The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack (...)
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  22. Massimo Pigliucci (2005). Evolution of Phenotypic Plasticity: Where Are We Going Now? Trends in Ecology and Evolution 20 (9):481-486.
    The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where (...)
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  23. Massimo Pigliucci (2003). Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. Ecology Letters 6:265-272.
    Phenotypic integration refers to the study of complex patterns of covariation among functionally related traits in a given organism. It has been investigated throughout the 20th century, but has only recently risen to the forefront of evolutionary ecological research. In this essay, I identify the reasons for this late flourishing of studies on integration, and discuss some of the major areas of current endeavour: the interplay of adaptation and constraints, the genetic and molecular bases of integration, the role of phenotypic (...)
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  24. Massimo Pigliucci (2003). From Molecules to Phenotypes? The Promise and Limits of Integrative Biology. Basic and Applied Ecology 4:297-306.
    Is integrative biology a good idea, or even possible? There has been much interest lately in the unifica- tion of biology and the integration of traditionally separate disciplines such as molecular and develop- mental biology on one hand, and ecology and evolutionary biology on the other. In this paper I ask if and under what circumstances such integration of efforts actually makes sense. I develop by example an analogy with Aristotle’s famous four “causes” that one can investigate concerning any object (...)
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  25. Massimo Pigliucci (2003). Genetic Assimilation and a Possible Evolutionary Paradox: Can Macroevolution Sometimes Be so Fast to Pass Us By? Evolution 57 (7):1455-1464.
    The idea of genetic assimilation, that environmentally induced phenotypes may become genetically fixed and no longer require the original environmental stimulus, has had varied success through time in evolutionary biology research. Proposed by Waddington in the 1940s, it became an area of active empirical research mostly thanks to the efforts of its inventor and his collaborators. It was then attacked as of minor importance during the ‘‘hardening’’ of the neo-Darwinian synthesis and was relegated to a secondary role for decades. Recently, (...)
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  26. Massimo Pigliucci (2003). Genetic Assimilation and a Possible Evolutionary Paradox: Can Macroevolution Sometimes Be so Fast to Pass Us By? Evolution 57 (7):1455-1464.
    The idea of genetic assimilation, that environmentally induced phenotypes may become genetically fixed and no longer require the original environmental stimulus, has had varied success through time in evolutionary biology research. Proposed by Waddington in the 1940s, it became an area of active empirical research mostly thanks to the efforts of its inventor and his collaborators. It was then attacked as of minor importance during the ‘‘hardening’’ of the neo-Darwinian synthesis and was relegated to a secondary role for decades. Recently, (...)
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  27. Massimo Pigliucci (2001). Phenotypic Plasticity. In C. W. Fox D. A. Roff (ed.), Evolutionary Ecology: Concepts and Case Studies.
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  28. Massimo Pigliucci, Courtney Murren & Carl Schlichting (2006). Phenotypic Plasticity and Evolution by Genetic Assimilation. Journal of Experimental Biology 209:2362-2367.
    In addition to considerable debate in the recent evolutionary literature about the limits of the Modern Synthesis of the 1930s and 1940s, there has also been theoretical and empirical interest in a variety of new and not so new concepts such as phenotypic plasticity, genetic assimilation and phenotypic accommodation. Here we consider examples of the arguments and counter- arguments that have shaped this discussion. We suggest that much of the controversy hinges on several misunderstandings, including unwarranted fears of a general (...)
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  29. Alexander Powell (2011). Book Review Essay of J. Shapiro, Evolution: A View From the 21st Century. [REVIEW] Genomics, Society and Policy 7:35-43.
  30. Christina Richards (2006). Jack of All Trades, Master of Some? On the Role of Phenotypic Plasticity in Plant Invasions. Ecology Letters 9:981-993.
    Invasion biologists often suggest that phenotypic plasticity plays an important role in successful plant invasions. Assuming that plasticity enhances ecological niche breadth and therefore confers a fitness advantage, recent studies have posed two main hypotheses: (1) invasive species are more plastic than non-invasive or native ones; (2) populations in the introduced range of an invasive species have evolved greater plasticity than populations in the native range. These two hypotheses largely reflect the disparate interests of ecologists and evolutionary biologists. Because these (...)
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  31. Carl Schlichting & Massimo Pigliucci (1998). Phenotypic Evolution: A Reaction Norm Perspective. Sinauer.
    Phenotypic Evolution explicitly recognizes organisms as complex genetic-epigenetic systems developing in response to changing internal and external environments. As a key to a better understanding of how phenotypes evolve, the authors have developed a framework that centers on the concept of the Developmental Reaction Norm. This encompasses their views: (1) that organisms are better considered as integrated units than as disconnected parts (allometry and phenotypic integration); (2) that an understanding of ontogeny is vital for evaluating evolution of adult forms (ontogenetic (...)
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  32. 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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  33. Marco Solinas (2008). Review of Jan-Christoph Heiliger (ed.), Naturgeschichte der Freiheit. [REVIEW] Iride (54):496-498.
  34. Arlin Stoltzfus (2012). Constructive Neutral Evolution: Exploring Evolutionary Theory's Curious Disconnect. Biology Direct 7:35.
    Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing (...)
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  35. Arlin Stoltzfus (2006). Mutationism and the Dual Causation of Evolutionary Change. Evolution and Development 8 (3):304-317.
    The rediscovery of Mendel's laws a century ago launched the science that William Bateson called "genetics," and led to a new view of evolution combining selection, particulate inheritance, and the newly characterized phenomenon of "mutation." This "mutationist" view clashed with the earlier view of Darwin, and the later "Modern Synthesis," by allowing discontinuity, and by recognizing mutation (or more properly, mutation-and-altered-development) as a source of creativity, direction, and initiative. By the mid-20th century, the opposing Modern Synthesis view was a prevailing (...)
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  36. Arlin Stoltzfus (1999). On the Possibility of Constructive Neutral Evolution. Journal of Molecular Evolution 49 (2):169-181.
    The neutral theory often is presented as a theory of "noise" or silent changes at an isolated "molecular level", relevant to marking the steady pace of divergence, but not to the origin of biological structure, function, or complexity. Nevertheless, precisely these issues can be addressed in neutral models, such as those elaborated here in regard to scrambled ciliate genes, gRNA-mediated RNA editing, the transition from self-splicing to spliceosomal splicing, and the retention of duplicate genes. All of these are instances of (...)
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  37. Arlin Stoltzfus & Lev Yampolsky (2009). Climbing Mount Probable: Mutation as a Cause of Non-Randomness in Evolution. Journal of Heredity 100 (5):637-647.
    The classic view of evolution as "shifting gene frequencies" in the Modern Synthesis literally means that evolution is the modulation of existing variation ("standing variation"), as opposed to a "new mutations" view of evolution as a 2-step process of mutational origin followed by acceptance-or-rejection (via selection and drift). The latter view has received renewed attention, yet its implications for evolutionary causation still are not widely understood. We review theoretical results showing that this conception of evolution allows for a role of (...)
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