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  1. Alfonso Arroyo-Santos & Mark E. Olson, Metaphors as Surrogate Variables. The Case of Adaptive Radiation.
    We develop a new metaphor account where metaphors become surrogate variables for different but related phenomena. As we will argue, subrogation is the result of the interplay between the things inspired by the metaphor and the empirical dynamics that result from such inspiration. In particular, we focus on adaptive radiation, a major concept of evolutionary biology. Our study suggests that there is no distinct phenomenon, process, or pattern in nature than can be identified as adaptive radiation. What we have instead (...)
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  2. Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva (2015). Practice-Oriented Controversies and Borrowed Epistemic Credibility in Current Evolutionary Biology: Phylogeography as a Case Study. Perspectives on Science 25 (3):310-334.
    Philosophical treatments of scientific controversies usually focus on theory, excluding important practice related aspects. However, scientists in conflict often appeal to extra-theoretical and extra-empirical elements. To understand better the role that non-empirical elements play in scientific controversies, we introduce the notion of borrowed epistemic credibility, illustrating our proposal with a recent controversy in a field of evolutionary biology known as phylogeography. Our analysis shows how scientific controversies that spring from disagreements about methodological issues potentially involve deeper debates regarding what constitutes (...)
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  3. Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva (2014). Practice-Oriented Controversies and Borrowed Epistemic Support in Current Evolutionary Biology: Phylogeography as a Case Study. Biology and Philosophy 29:833-850.
    Although there is increasing recognition that theory and practice in science are often inseparably intertwined, discussions of scientific controversies often continue to focus on theory, and not practice or methodologies. As a contribution to constructing a framework towards understanding controversies linked to scientific practices, we introduce the notion of borrowed epistemic credibility, to describe the situation in which scientists exploit fallacious similarities between accepted tenets in other fields to garner support for a given position in their own field. Our proposal (...)
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  4. 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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  5. Ellen Clarke, The Evolution of Cooperation. The Philosophers' Magazine.
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  6. 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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  7. Charles Darwin (1967). L'origine delle specie. Boringhieri.
  8. 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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  9. 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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  10. 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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  11. 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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  12. Gary Hatfield (2008). Animals. In John Carriero & Janet Broughton (eds.), Companion to Descartes. Blackwell 404–425.
    This chapter considers philosophical problems concerning non-human (and sometimes human) animals, including their metaphysical, physical, and moral status, their origin, what makes them alive, their functional organization, and the basis of their sensitive and cognitive capacities. I proceed by assuming what most of Descartes’s followers and interpreters have held: that Descartes proposed that animals lack sentience, feeling, and genuinely cognitive representations of things. (Some scholars interpret Descartes differently, denying that he excluded sentience, feeling, and representation from animals, and I consider (...)
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  13. 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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  14. 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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  15. 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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  16. 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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  17. Ehud Lamm & Ohad Kammar (2014). Inferring Coevolution. Philosophy of Science 81 (4):592-611.
    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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  18. Charles H. Lineweaver, Paul C. W. Davies & Michael Ruse (eds.) (2013). Complexity and the Arrow of Time. Cambridge U.P..
  19. Lucas J. Matthews (2016). On Closing the Gap Between Philosophical Concepts and Their Usage in Scientific Practice: A Lesson From the Debate About Natural Selection as a Mechanism. Studies in History and Philosophy of Science Part C 55:21-28.
    In addition to theorizing about the role and value of mechanisms in scientific explanation or the causal structure of the world, there is a fundamental task of getting straight what a ‘mechanism’ is in the first place. Broadly, this paper is about the challenge of application: the challenge of aligning one's philosophical account of a scientific concept with the manner in which that concept is actually used in scientific practice. This paper considers a case study of the challenge of (...)
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  20. 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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  21. 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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  22. Nicholas Maxwell (1984). The Generalized Darwinian Research Programme. In From Knowledge to Wisdom. Blackwell 269-275.
    The generalized Darwinian research programme accepts physicalism, but holds that all life is purposive in character. It seeks to understand how and why all purposiveness has evolved in the universe – especially purposiveness associated with what we value most in human life, such as sentience, consciousness, person-to-person understanding, science, art, free¬dom, love. As evolution proceeds, the mechanisms of evolution themselves evolve to take into account the increasingly important role that purposive action can play - especially when quasi-Lamarckian evolution by cultural (...)
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  23. 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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  24. 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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  25. 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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  26. 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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  27. Giuseppe Montalenti (1967). Introduzione a Charles Darwin, L'origine delle specie. Boringhieri.
  28. Giuseppe Montalenti (1965-1982). L'evoluzione. Einaudi.
  29. Giuseppe Montalenti (1965-1982). L'evoluzione. Einaudi.
  30. Giuseppe Montalenti (1965-1982). L'evoluzione. Einaudi.
  31. Giuseppe Montalenti (1965-1982). L'evoluzione. Einaudi.
  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. Massimo Pigliucci (2001). Phenotypic Plasticity. In C. W. Fox D. A. Roff (ed.), Evolutionary Ecology: Concepts and Case Studies.
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  42. 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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  43. Alexander Powell (2011). Book Review Essay of J. Shapiro, Evolution: A View From the 21st Century. [REVIEW] Genomics, Society and Policy 7:35-43.
  44. 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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  45. 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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  46. 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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  47. Marco Solinas (2008). Review of Jan-Christoph Heiliger (ed.), Naturgeschichte der Freiheit. [REVIEW] Iride (54):496-498.
  48. 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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  49. 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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  50. 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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