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  1. Rebecca Rogers Ackermann & James M. Cheverud (2004). Morphological Integration in Primate Evolution. In Massimo Pigliucci & Katherine Preston (eds.), Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. Oxford University Press
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  2. Mauro Adenzato (2000). Gene-Culture Coevolution Does Not Replace Standard Evolutionary Theory. Behavioral and Brain Sciences 23 (1):146-146.
    Though the target article is not without fertile suggestions, at least two problems limit its overall validity: (1) the extended gene-culture coevolutionary framework is not an alternative to standard evolutionary theory; (2) the proposed model does not explain how much time is necessary for selective pressure to determine the stabilization of a new aspect of the genotype.
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  3. Joseph S. Alper (1995). Does the ADA Provide Protection Against Discrimination on the Basis of Genotype? Journal of Law, Medicine & Ethics 23 (2):167-172.
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  4. Robert Aunger (2006). Culture Evolves Only If There is Cultural Inheritance. Behavioral and Brain Sciences 29 (4):347-348.
    Mesoudi et al. argue that the current inability to identify the means by which cultural traits are acquired does not debilitate their project to draw clear parallels between cultural and biological evolution. However, I suggest that cultural phenomena may be accounted for by biological processes, unless we can identify a cultural “genotype” that carries information from person to person independently of genes. (Published Online November 9 2006).
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  5. Christopher J. Austin (2015). The Dispositional Genome: Primus Inter Pares. Biology and Philosophy 30 (2):227-246.
    According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as “first among equals” with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology - the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly “environmental” factors. Parting with the methodology of the popular responses to the Thesis, this paper offers (...)
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  6. Carl T. Bergstrom & Peter Godfrey-Smith (1998). On the Evolution of Behavioral Complexity in Individuals and Populations. Biology and Philosophy 13 (2):205-31.
    A wide range of ecological and evolutionary models predict variety in phenotype or behavior when a population is at equilibrium. This heterogeneity can be realized in different ways. For example, it can be realized through a complex population of individuals exhibiting different simple behaviors, or through a simple population of individuals exhibiting complex, varying behaviors. In some theoretical frameworks these different realizations are treated as equivalent, but natural selection distinguishes between these two alternatives in subtle ways. By investigating an increasingly (...)
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  7. Ken Binmore (2013). Sexual Drift. Biological Theory 8 (2):201-208.
    This paper uses a 4 × 4 expansion of the Hawk–Dove Game to illustrate how sexual drift in a large genotype space can shift a population from one equilibrium in a smaller phenotype space to another. An equilibrium is only safe from being destabilized in this way when implemented by recessive alleles.
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  8. Marion Blute (2001). A Single-Process Learning Theory. Behavioral and Brain Sciences 24 (3):529-531.
    Many analogies exist between the process of evolution by natural selection and of learning by reinforcement and punishment. A full extension of the evolutionary analogy to learning to include analogues of the fitness, genotype, development, environmental influences, and phenotype concepts makes possible a single theory of the learning process able to encompass all of the elementary procedures known to yield learning.
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  9. Sylvia Culp (1997). Establishing Genotype/Phenotype Relationships: Gene Targeting as an Experimental Approach. Philosophy of Science 64 (4):278.
    In this paper, I examine an experimental technique, gene targeting, used for establishing genotype/phenotype relationships. Through analyzing a case study, I identify many pitfalls that may lead to false conclusions about these relationships. I argue that some of these pitfalls may seriously affect gene targeting's usefulness for associating phenotypes with genes cataloged by the Human Genome Project. This case also shows the use of gene targeted mice as model systems for studying genotype/phenotype relationships in humans. Moreover, I argue that it (...)
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  10. Marie Darrason (2013). Unifying Diseases From a Genetic Point of View: The Example of the Genetic Theory of Infectious Diseases. Theoretical Medicine and Bioethics 34 (4):327-344.
    In the contemporary biomedical literature, every disease is considered genetic. This extension of the concept of genetic disease is usually interpreted either in a trivial or genocentrist sense, but it is never taken seriously as the expression of a genetic theory of disease. However, a group of French researchers defend the idea of a genetic theory of infectious diseases. By identifying four common genetic mechanisms (Mendelian predisposition to multiple infections, Mendelian predisposition to one infection, and major gene and polygenic predispositions), (...)
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  11. Andrew R. Deans, Barry Smith & Others (2015). Finding Our Way Through Phenotypes. PLoS Biology 13 (1).
    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...)
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  12. Raphael Falk (1993). Evolutionary Epistemology: What Phenotype is Selected and Which Genotype Evolves? Biology and Philosophy 8 (2):153-172.
    In 1941/42 Konrad Lorenz suggested that Kant's transcendental categories ofa priori knowledge could be given an empirical interpretation in Darwinian material evolutionary terms: a priori propositional knowledge was an organ subject to natural selection for adaptation to its specific environments. D. Campbell extended the conception, and termed evolution a process of knowledge. The philosophical problem of what knowledge is became a descriptive one of how knowledge developed, the normative semantic questions have been sidestepped, as if the descriptive insights would automatically (...)
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  13. Laura Gangoso, Rocío Márquez‐Ferrando, Francisco Ramírez, Ivan Gomez‐Mestre & Jordi Figuerola (2013). Understanding Phenotypic Responses to Global Change. Bioessays 35 (5):491-495.
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  14. W. Godfrey-Smith (1980). Book Reviews. [REVIEW] Philosophical Quarterly 30 (121):356.
    KAPIAN J.M. 8t PIGLIUcci, M. (2001). Genes "for" phenotypes: a modern history view. Bi- ology and Philosophy, 16, 189 — 213. PIOLIUcci, M. (2003). From molecules to phenotypes? The promise and limits of integrative biology. Basic and Applied Ecology, 4, 297— 306. WAGNER, G.P. (2001). The character concept in..
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  15. Kai Hahlweg (1981). Progress Through Evolution? An Inquiry Into the Thought of C.H. Waddington. Acta Biotheoretica 30 (2):103-120.
    It was C.H. Waddington's contention that the Neo-Darwinian Theory of Evolution ought to be amended by imbedding it in a broader theoretical framework which takes the role of the phenotype into account. Waddington's theory alleges the existence of two interlocking feedback circuits between environment and phenotype on the one hand and genotype and phenotype on the other. The resulting dynamical model of evolutionary change gives new meaning to the notion of progress in evolution. In this model natural selection acts directly (...)
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  16. David Haig (2007). Weismann Rules! OK? Epigenetics and the Lamarckian Temptation. Biology and Philosophy 22 (3):415-428.
    August Weismann rejected the inheritance of acquired characters on the grounds that changes to the soma cannot produce the kind of changes to the germ-plasm that would result in the altered character being transmitted to subsequent generations. His intended distinction, between germ-plasm and soma, was closer to the modern distinction between genotype and phenotype than to the modern distinction between germ cells and somatic cells. Recently, systems of epigenetic inheritance have been claimed to make possible the inheritance of acquired characters. (...)
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  17. Brian K. Hall (2003). Unlocking the Black Box Between Genotype and Phenotype: Cell Condensations as Morphogenetic (Modular) Units. [REVIEW] Biology and Philosophy 18 (2):219-247.
    Embryonic development and ontogeny occupy whatis often depicted as the black box betweengenes – the genotype – and the features(structures, functions, behaviors) of organisms– the phenotype; the phenotype is not merelya one-to-one readout of the genotype. Thegenes home, context, and locus of operation isthe cell. Initially, in ontogeny, that cell isthe single-celled zygote. As developmentensues, multicellular assemblages of like cells(modules) progressively organized as germlayers, embryonic fields, anlage,condensations, or blastemata, enable genes toplay their roles in development and evolution.As modules, condensations are (...)
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  18. E. Jablonka (2004). From Replicators to Heritably Varying Phenotypic Traits: The Extended Phenotype Revisited. [REVIEW] Biology and Philosophy 19 (3):353-375.
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  19. Kevin N. Laland (2004). Extending the Extended Phenotype. Biology and Philosophy 19 (3):313-325.
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  20. Romain Laurent & Raphaëlle Chaix (2012). HapMap European American Genotypes Are Compatible with the Hypothesis of MHC‐Dependent Mate Choice (Response to DOI 10.1002/Bies. 201200023, Derti and Roth). [REVIEW] Bioessays 34 (10):871-872.
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  21. Piotr Lenartowicz (1975). Phenotype-Genotype Dichotomy: An Essay in Theoretical Biology. Typis Pontificiae Universitatis Gregorianae.
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  22. Bradford Z. Mahon (2003). The Genetics of Environment and the Environment of Genotypes. Social Philosophy Today 19:79-87.
    In this paper I discuss one possible extension of Richard Lewontin’s proposal in The Triple Helix. After reviewing the theoretical commitments common to discussions that assume we will be able to compute an organism from its genes, I turn to Lewontin’s arguments that we will never be able to compute phenotype from genotype because the genotype specifies an organism’s phenotype relative to a range of environments. The focus of the discussion in this paper, however, is on what might follow if (...)
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  23. Gerry McDermott, Douglas M. Fox, Lindsay Epperly, Modi Wetzler, Annelise E. Barron, Mark A. Le Gros & Carolyn A. Larabell (2012). Visualizing and Quantifying Cell Phenotype Using Soft X‐Ray Tomography. Bioessays 34 (4):320-327.
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  24. Stephen S. Morse (1992). Evolving Views of Viral Evolution: Towards an Evolutionary Biology of Viruses. History and Philosophy of the Life Sciences 14 (2):215 - 248.
    Despite considerable interest in viral evolution, at least among virologists, viruses are rarely considered from the same evolutionary vantage point as other organisms. Early work of necessity emphasized phenotype and phenotypic variation (and therefore arguably was more oriented towards the broader biological and ecological perspectives). More recent work (essentially since the development of molecular evolution in the 1960's but beginning earlier) has concentrated on genotypic variation, with less clarity about the significance of such variations. Other aspects of evolutionary theory, especially (...)
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  25. Ohad Nachtomy, Yaron Ramati, Ayelet Shavit & Zohar Yakhini (2009). It Takes Two to Tango: Genotyping and Phenotyping in Genome-Wide Association Studies. Biological Theory 4 (3):294-301.
    In this article we examine the “phenotype” concept in light of recent technological advances in Genome-Wide Association Studies . By observing the technology and its presuppositions, we put forward the thesis that at least in this case genotype and phenotype are effectively coidentifled one by means of the other. We suggest that the coidentiflcation of genotype-phenotype couples in expression-based GWAS also indicates a conceptual dependence, which we call “co-deñnition.” We note that viewing these terms as codeflned runs against possible expectations, (...)
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  26. Karen Neander (1995). Pruning the Tree of Life. British Journal for the Philosophy of Science 46 (1):59-80.
    argue that natural selection does not explain the genotypic arid phenotypic properties of individuals. On this view, natural selection explains the adaptedness of individuals, not by explaining why the individuals that exist have the adaptations they do, but rather by explaining why the individuals that exist are the ones with those adaptations. This paper argues that this ‘Negative’ view of natural selection ignores the fact that natural selection is a cumulative selection process. So understood, it explains how the genetic sequences (...)
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  27. Gry Oftedal (2005). Heritability and Genetic Causation. Philosophy of Science 72 (5):699-709.
    The method in human genetics of ascribing causal responsibility to genotype by the use of heritability estimates has been heavily criticized over the years. It has been argued that these estimates are rarely valid and do not serve the purpose of tracing genetic causes. Recent contributions strike back at this criticism. I present and discuss two opposing views on these matters represented by Richard Lewontin and Neven Sesardic, and I suggest that some of the disagreement is based on differing concepts (...)
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  28. Yin Paradies, M. J. Montoya & Stephanie M. Fullerton (2007). Racialized Genetics and the Study of Complex Diseases: The Thrifty Genotype Revisited. Perspectives in Biology and Medicine 50 (2):203-227.
  29. Charles H. Pence (2015). Military Genomic Testing: Proportionality, Expected Benefits, and the Connection Between Genotypes and Phenotypes. Journal of Law and the Biosciences 2 (1):85-91.
    Mehlman and Li offer a framework for approaching the bioethical issues raised by the military use of genomics that is compellingly grounded in both the contemporary civilian and military ethics of medical research, arguing that military commanders must be bound by the two principles of paternal- ism and proportionality. I agree fully. But I argue here that this is a much higher bar than we may fully realize. Just as the principle of proportionality relies upon a thorough assessment of harms (...)
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  30. Massimo Pigliucci (2010). Genotype–Phenotype Mapping and the End of the ‘Genes as Blueprint’ Metaphor. Philosophical Transactions Royal Society B 365:557–566.
    In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...)
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  31. Andreas Rechtsteiner, Mark A. Bedau.
    We introduce and study a simple generic model of neutral evolution of genotypes, designed to provide a feasible and general method for quantifying excess evolutionary activity|the extent to which evolutionary activity is the product of adaptive evolution. We compare the behavior of the generic neutral model against two other models: Packard's agent-based model of the evolution of sensory-motor functionality and a neutral \shadow" of Packard's model. Diversity and evolutionary activity of these three models across the mutation rate spectrum illustrate the (...)
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  32. Nils Roll-Hansen (2009). Sources of Wilhelm Johannsen's Genotype Theory. Journal of the History of Biology 42 (3):457 - 493.
    This paper describes the historical background and early formation of Wilhelm Johannsen's distinction between genotype and phenotype. It is argued that contrary to a widely accepted interpretation (For instance, W. Provine, 1971. "The Origins of Theoretical Population Genetics". Chicago: The University of Chicago Press; Mayr, 1973; F. B. Churchill, 1974. "Journal of the History of Biology" 7: 5-30; E. Mayr, 1982. "The Growth of Biological Thought," Cambridge: Harvard University Press; J. Sapp, 2003. Genesis. "The Evolution of Biology". New York: Oxford (...)
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  33. Alirio Rosales (2005). John Maynard Smith and the Natural Philosophy of␣Adaptation. Biology and Philosophy 20 (5):1027-1040.
    One of the most remarkable aspects of John Maynard Smith’s work was the fact that he devoted time both to doing science and to reflecting philosophically upon its methods and concepts. In this paper I offer a philosophical analysis of Maynard Smith’s approach to modelling phenotypic evolution in relation to three main themes. The first concerns the type of scientific understanding that ESS and optimality models give us. The second concerns the causal–historical aspect of stability analyses of adaptation. The third (...)
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  34. Suzanne L. Rutherford (2000). From Genotype to Phenotype: Buffering Mechanisms and the Storage of Genetic Information. Bioessays 22 (12):1095-1105.
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  35. Sahotra Sarkar & Trevon Fuller, Generalized Norms of Reaction for Ecological Developmental Biology.
    A standard norm of reaction (NoR) is a graphical depiction of the phenotypic value of some trait of an individual genotype in a population as a function of an environmental parameter. NoRs thus depict the phenotypic plasticity of a trait. The topological properties of NoRs for sets of different genotypes can be used to infer the presence of (non-linear) genotype-environment interactions. While it is clear that many NoRs are adaptive, it is not yet settled whether their evolutionary etiology should be (...)
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  36. Neven Sesardic (1993). Heritability and Causality. Philosophy of Science 60 (3):396-418.
    The critics of "hereditarianism" often claim that any attempt to explain human behavior by invoking genes is confronted with insurmountable methodological difficulties. They reject the idea that heritability estimates could lead to genetic explanations by pointing out that these estimates are strictly valid only for a given population and that they are exposed to the irremovable confounding effects of genotype-environment interaction and genotype-environment correlation. I argue that these difficulties are greatly exaggerated, and that we would be wrong to regard them (...)
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  37. Elliott Sober (1992). Screening-Off and the Units of Selection. Philosophy of Science 59 (1):142-152.
    Brandon ([1982] 1984, 1990) has argued that Salmon's (1971) concept of screening-off can be used to characterize (i) the idea that natural selection acts directly on an organism's phenotype, only indirectly on its genotype, and (ii) the biological problem of the levels of selection. Brandon also suggests (iii) that screening-off events in a causal chain are better explanations than the events they screen off. This paper critically evaluates Brandon's proposals.
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  38. Peter F. Stadler & Bärbel M. R. Stadler (2006). Genotype?Phenotype Maps. Biological Theory 1 (3):268-279.
    The current implementation of the Neo-Darwinian model of evolution typically assumes that the set of possible phenotypes is organized into a highly symmetric and regular space. Most conveniently, a Euclidean vector space is used, representing phenotypic properties by real-valued variables. Computational work on the biophysical genotype-phenotype model of RNA folding, however, suggests a rather different picture. If phenotypes are organized according to genetic accessibility, the resulting space lacks a metric and can be formalized only in terms of a relatively unfamiliar (...)
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  39. James Tabery (2008). R. A. Fisher, Lancelot Hogben, and the Origin(s) of Genotype-Environment Interaction. Journal of the History of Biology 41 (4):717 - 761.
    This essay examines the origin(s) of genotype-environment interaction, or G×E. "Origin(s)" and not "the origin" because the thesis is that there were actually two distinct concepts of G×E at this beginning: a biometric concept, or \[G \times E_B\] , and a developmental concept, or \[G \times E_D \] . R. A. Fisher, one of the founders of population genetics and the creator of the statistical analysis of variance, introduced the biometric concept as he attempted to resolve one of the main (...)
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  40. J. Scott Turner (2004). Extended Phenotypes and Extended Organisms. Biology and Philosophy 19 (3):327-352.
    Phenotype, whether conventional or extended, is defined as a reflectionof an underlying genotype. Adaptation and the natural selection thatfollows from it depends upon a progressively harmonious fit betweenphenotype and environment. There is in Richard Dawkins' notion ofthe extended phenotype a paradox that seems to undercut conventionalviews of adaptation, natural selection and adaptation. In a nutshell, ifthe phenotype includes an organism's environment, how then can theorganism adapt to itself? The paradox is resolvable through aphysiological, as opposed to a genetic, theory of (...)
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  41. Andreas Wagner (2011). The Low Cost of Recombination in Creating Novel Phenotypes. Bioessays 33 (8):636-646.
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  42. Degeng Wang (2005). “Molecular Gene”: Interpretation in the Right Context. [REVIEW] Biology and Philosophy 20 (2-3):453-464.
    How to interpret the “molecular gene” concept is discussed in this paper. I argue that the architecture of biological systems is hierarchical and multi-layered, exhibiting striking similarities to that of modern computers. Multiple layers exist between the genotype and system level property, the phenotype. This architectural complexity gives rise to the intrinsic complexity of the genotype-phenotype relationships. The notion of a gene being for a phenotypic trait or traits lacks adequate consideration of this complexity and has limitations in explaining the (...)
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  43. John S. Wilkins, Ian Musgrave & Clem Stanyon (2012). Selection Without Replicators: The Origin of Genes, and the Replicator/Interactor Distinction in Etiobiology. Biology and Philosophy 27 (2):215-239.
    Genes are thought to have evolved from long-lived and multiply-interactive molecules in the early stages of the origins of life. However, at that stage there were no replicators, and the distinction between interactors and replicators did not yet apply. Nevertheless, the process of evolution that proceeded from initial autocatalytic hypercycles to full organisms was a Darwinian process of selection of favourable variants. We distinguish therefore between Neo-Darwinian evolution and the related Weismannian and Central Dogma divisions, on the one hand, and (...)
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  44. Neil A. Youngson, Suyinn Chong & Emma Whitelaw (2011). Gene Silencing is an Ancient Means of Producing Multiple Phenotypes From the Same Genotype. Bioessays 33 (2):95-99.
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