Results for 'lineage-specific biology'

993 found
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  1.  6
    Lineagespecific genomics: Frequent birth and death in the human genome.Robert S. Young - 2016 - Bioessays 38 (7):654-663.
    Frequent evolutionary birth and death events have created a large quantity of biologically important, lineagespecific DNA within mammalian genomes. The birth and death of DNA sequences is so frequent that the total number of these insertions and deletions in the human population remains unknown, although there are differences between these groups, e.g. transposable elements contribute predominantly to sequence insertion. Functional turnover – where the activity of a locus is specific to one lineage, but the underlying DNA (...)
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  2.  23
    A panorama of lineagespecific transcription in hematopoiesis.Yuval Kluger, Zheng Lian, Xueqing Zhang, Peter E. Newburger & Sherman M. Weissman - 2004 - Bioessays 26 (12):1276-1287.
    The hematopoietic system consists of more than ten differentiated cell types, all of which are derived from a single type of hematopoietic stem cell. The accessibility and interest of this system have made it a model for understanding normal and abnormal differentiation of mammalian cells. Newer techniques have generated a mass of data that requires integrative approaches for analysis and interpretation. The traditional view of the differentiation program holds that a small number of regulators are involved in each stage of (...)
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  3.  42
    Gravity Constraints Drive Biological Systems Toward Specific Organization Patterns.Mariano Bizzarri, Maria Grazia Masiello, Alessandro Giuliani & Alessandra Cucina - 2018 - Bioessays 40 (1):1700138.
    Different cell lineages growing in microgravity undergo a spontaneous transition leading to the emergence of two distinct phenotypes. By returning these populations in a normal gravitational field, the two phenotypes collapse, recovering their original configuration. In this review, we hypothesize that, once the gravitational constraint is removed, the system freely explores its phenotypic space, while, when in a gravitational field, cells are “constrained” to adopt only one favored configuration. We suggest that the genome allows for a wide range of “possibilities” (...)
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  4. Stem Cell Lineages: Between Cell and Organism.Melinda Bonnie Fagan - 2017 - Philosophy, Theory, and Practice in Biology 9 (6).
    Ontologies of living things are increasingly grounded on the concepts and practices of current life science. Biological development is a process, undergone by living things, which begins with a single cell and (in an important class of cases) ends with formation of a multicellular organism. The process of development is thus prima facie central for ideas about biological individuality and organismality. However, recent accounts of these concepts do not engage developmental biology. This paper aims to fill the gap, proposing (...)
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  5.  35
    Human phenotypic morality and the biological basis for knowing good.Margaret Boone Rappaport & Christopher Corbally - 2017 - Zygon 52 (3):822-846.
    Co-creating knowledge takes a new approach to human phenotypic morality as a biologically based, human lineage specific trait. Authors from very different backgrounds first review research on the nature and origins of morality using the social brain network, and studies of individuals who cannot “know good” or think morally because of brain dysfunction. They find these models helpful but insufficient, and turn to paleoanthropology, cognitive science, and neuroscience to understand human moral capacity and its origins long ago, in (...)
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  6.  6
    Another notch in stem cell biology: Drosophila intestinal stem cells and the specification of cell fates.Andrew A. Wilson & Darrell N. Kotton - 2008 - Bioessays 30 (2):107-109.
    Previous work has suggested that many stem cells can be found in microanatomic niches, where adjacent somatic cells of the niche control the differentiation and proliferation states of their resident stem cells. Recently published work examining intestinal stem cells (ISCs) in the adult Drosophila midgut suggests a new paradigm where some stem cells actively control the cell fate decisions of their daughters. Here, we review recent literature(1) demonstrating that, in the absence of a detectable stem cell niche, multipotent Drosophila ISCs (...)
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  7.  24
    Biological Boundaries and the Vertebrate Immune System.Julio R. Tuma - 2009 - Biological Theory 4 (3):287-293.
    Biological boundaries are important because of what they reveal about the evolution of a lineage, the relationship between organisms of different lineages, the structure and function of particular subsystems of the organism, the interconnection between an organism and its environment, and a myriad of other important issues related to individuality, development, and evolution. Since there is no single unifying theory for all biological sciences, there are various possible theoretical characterizations of what counts as a biological boundary. Theoretical specificity is (...)
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  8.  19
    Homology of process: developmental dynamics in comparative biology.James DiFrisco & Johannes Jaeger - forthcoming - Interface Focus.
    Comparative biology builds up systematic knowledge of the diversity of life, across evolutionary lineages and levels of organization, starting with evidence from a sparse sample of model organisms. In developmental biology, a key obstacle to the growth of comparative approaches is that the concept of homology is not very well defined for levels of organization that are intermediate between individual genes and morphological characters. In this paper, we investigate what it means for ontogenetic processes to be homologous, focusing (...)
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  9.  89
    Explanatory Integration Challenges in Evolutionary Systems Biology.Sara Green, Melinda Fagan & Johannes Jaeger - 2015 - Biological Theory 10 (1):18-35.
    Evolutionary systems biology (ESB) aims to integrate methods from systems biology and evolutionary biology to go beyond the current limitations in both fields. This article clarifies some conceptual difficulties of this integration project, and shows how they can be overcome. The main challenge we consider involves the integration of evolutionary biology with developmental dynamics, illustrated with two examples. First, we examine historical tensions between efforts to define general evolutionary principles and articulation of detailed mechanistic explanations of (...)
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  10.  20
    Human and primate‐specific microRNAs in cancer: Evolution, and significance in comparison with more distantly‐related research models.Costas Koufaris - 2016 - Bioessays 38 (3).
    The largest proportion of microRNAs in humans (ca. 40–50%) originated in the phylogenetic grouping defined as primates. The dynamic evolution of this family of non‐coding RNA is further demonstrated by the presence of microRNA unique to the human species. Investigations into the role of microRNA in cancer have until recently mainly focused on the more ancient members of this RNA family that are widely conserved in the animal kingdom. As I describe in this review the evolutionary young lineage and (...)
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  11.  22
    Form and Order in Evolutionary Biology: Stuart Kauffman's Transformation of Theoretical Biology.Richard M. Burian & Robert C. Richardson - 1990 - PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1990:267 - 287.
    The formal framework of Kauffman (1991) depicts the constraints of self-organization on the evolution of complex systems and the relation of self-organization to selection. We discuss his treatment of 'generic constraints' as sources of order (section 2) and the relation between adaptation and organization (section 3). We then raise a number of issues, including the role of adaptation in explaining order (section 4) and the limitations of formal approaches in explaining the distinctively biological (section 5). The principal question we pose (...)
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  12.  15
    Understanding fundamental principles of enhancer biology at a model locus.Mira Kassouf, Seren Ford, Joseph Blayney & Doug Higgs - 2023 - Bioessays 45 (10):2300047.
    Despite ever‐increasing accumulation of genomic data, the fundamental question of how individual genes are switched on during development, lineage‐specification and differentiation is not fully answered. It is widely accepted that this involves the interaction between at least three fundamental regulatory elements: enhancers, promoters and insulators. Enhancers contain transcription factor binding sites which are bound by transcription factors (TFs) and co‐factors expressed during cell fate decisions and maintain imposed patterns of activation, at least in part, via their epigenetic modification. This (...)
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  13.  25
    Extending the Explanatory Scope of Evolutionary Theory: The Origination of Historical Kinds in Biology and Culture.Günter P. Wagner & Gary Tomlinson - 2022 - Philosophy, Theory, and Practice in Biology 14 (1).
    Two welcome extensions of evolutionary thinking have come to prominence over the last thirty years: the so-called ’extended evolutionary synthesis’ (EES) and debate about biological kinds and individuals. These two agendas have, however, remained orthogonal to one another. The EES has mostly restricted itself to widening the explanations of adaptation offered by the preceding ’modern evolutionary synthesis’ by including additional mechanisms of inheritance and variation; while discussion of biological kinds has turned toward philosophical questions of essential vs. contingent properties of (...)
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  14.  50
    A Recapitulation of the Rise and Fall of the Cell Lineage Research Program: The Evolutionary-Developmental Relationship of Cleavage to Homology, Body Plans and Life History. [REVIEW]Robert Guralnick - 2002 - Journal of the History of Biology 35 (3):537 - 567.
    American biologists in the late nineteenth century pioneered the descriptive-comparative study of all cell divisions from zygote to gastrulation -- the cell lineage. Data from cell lineages were crucial to evolutionary and developmental questions of the day. One of the main questions was the ultimate causation of developmental patterns -- historical or mechanical. E. B. Wilson's groundbreaking lineage work on the polychaete worm Nereis in 1892 set the stage for (1) an attack on Haeckel's phylogenetic-historical notion of recapitulation (...)
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  15.  57
    From 2R to 3R: evidence for a fish‐specific genome duplication (FSGD).Axel Meyer & Yves Van de Peer - 2005 - Bioessays 27 (9):937-945.
    An important mechanism for the evolution of phenotypic complexity, diversity and innovation, and the origin of novel gene functions is the duplication of genes and entire genomes. Recent phylogenomic studies suggest that, during the evolution of vertebrates, the entire genome was duplicated in two rounds (2R) of duplication. Later, ∼350 mya, in the stem lineage of ray‐finned (actinopterygian) fishes, but not in that of the land vertebrates, a third genome duplication occurred—the fish‐specific genome duplication (FSGD or 3R), leading, (...)
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  16.  49
    The Homoscleromorph sponge Oscarellalobularis, a promising sponge model in evolutionary and developmental biology.Alexander V. Ereskovsky, Carole Borchiellini, Eve Gazave, Julijana Ivanisevic, Pascal Lapébie, Thierry Perez, Emmanuelle Renard & Jean Vacelet - 2009 - Bioessays 31 (1):89-97.
    Sponges branch basally in the metazoan phylogenetic tree and are believed to be composed of four distinct lineages with still uncertain relationships. Indeed, some molecular studies propose that Homoscleromorpha may be a fourth Sponge lineage, distinct from Demospongiae in which they were traditionally classified. They harbour many features that distinguish them from other sponges and are more evocative of those of the eumetazoans. They are notably the only sponges to possess a basement membrane with collagen IV and specialized cell‐junctions, (...)
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  17.  8
    Causing and Composing Evolution: Lessons from Evo-Devo Mechanisms.Cristina Villegas - 2023 - In João L. Cordovil, Gil Santos & Davide Vecchi (eds.), New Mechanism Explanation, Emergence and Reduction. Springer. pp. 61-83.
    Evolutionary developmental biology (evo-devo) is often vindicated by theoreticians of the field as a mechanistic science that brings a mechanistic perspective into evolutionary biology. Usually, it is also portrayed as stressing the causal role that development plays in the evolutionary process. However, mechanistic studies in evo-devo typically refer to lineage-specific transformations and lack the generality that evolutionary explanations usually aim for. After reviewing the prospects and limits of a mechanistic view of evo-devo and their studies of (...)
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  18.  18
    The Ciona intestinalis genome: When the constraints are off.Linda Z. Holland & Jeremy J. Gibson-Brown - 2003 - Bioessays 25 (6):529-532.
    The recent genome sequencing of a non‐vertebrate deuterostome, the ascidian tunicate Ciona intestinalis, makes a substantial contribution to the fields of evolutionary and developmental biology.1 Tunicates have some of the smallest bilaterian genomes, embryos with relatively few cells, fixed lineages and early determination of cell fates. Initial analyses of the C. intestinalis genome indicate that it has been evolving rapidly. Comparisons with other bilaterians show that C. intestinalis has lost a number of genes, and that many genes linked together (...)
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  19.  44
    Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica.Sreenivas Chavali, David A. De Lima Morais, Julian Gough & M. Madan Babu - 2011 - Bioessays 33 (8):592-601.
    Recent sequencing of the metazoan Oikopleura dioica genome has provided important insights, which challenges the current understanding of eukaryotic genome evolution. Many genomic features of O. dioica show deviation from the commonly observed trends in other eukaryotic genomes. For instance, O. dioica has a rapidly evolving, highly compact genome with a divergent intron‐exon organization. Additionally, O. dioica lacks the minor spliceosome and key DNA repair pathway genes. Even with a compact genome, O. dioica contains tandem repeats, comparable to other eukaryotes, (...)
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  20. Causal Specificity, Biological Possibility and Non-parity about Genetic Causes.Marcel Weber - manuscript
    Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...)
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  21. Species in the Age of Discordance.Matthew H. Haber - 2019 - Philosophy, Theory, and Practice in Biology 11 (21).
    Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, if (...)
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  22.  25
    Conditional Grandmother Effects on Age at Marriage, Age at First Birth, and Completed Fertility of Daughters and Daughters-in-law in Historical Krummhörn.Johannes Johow & Eckart Voland - 2012 - Human Nature 23 (3):341-359.
    Based on historical data pertaining to the Krummhörn population (eighteenth and nineteenth centuries, Germany), we compared reproductive histories of mothers according to whether the maternal grandmother (MGM) or the paternal grandmother (PGM) or neither of them was resident in the parents’ parish at the time of the mother’s first birth. In contrast to effects of PGMs, we discovered conditional differences in the MGM’s effects between landless people and wealthier, commercial farmers. Our data indicate that the presence of the MGM only (...)
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  23.  2
    Endothelial ontogeny and the establishment of vascular heterogeneity.Oliver A. Stone, Bin Zhou, Kristy Red-Horse & Didier Y. R. Stainier - 2021 - Bioessays 43 (7):2100036.
    The establishment of distinct cellular identities was pivotal during the evolution of Metazoa, enabling the emergence of an array of specialized tissues with different functions. In most animals including vertebrates, cell specialization occurs in response to a combination of intrinsic (e.g., cellular ontogeny) and extrinsic (e.g., local environment) factors that drive the acquisition of unique characteristics at the single‐cell level. The first functional organ system to form in vertebrates is the cardiovascular system, which is lined by a network of endothelial (...)
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  24.  25
    Factor mediated gene priming in pluripotent stem cells sets the stage for lineage specification.Niall Dillon - 2012 - Bioessays 34 (3):194-204.
    Priming of lineagespecific genes in pluripotent embryonic stem cells facilitates rapid and coordinated activation of transcriptional programmes during differentiation. There is growing evidence that pluripotency factors play key roles in priming tissue‐specific genes and in the earliest stages of lineage commitment. As differentiation progresses, pluripotency factors are replaced at some primed genes by related lineagespecific factors that bind to the same sequences and maintain epigenetic priming until the gene is activated. Polycomb and trithorax group (...)
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  25. Rethinking hereditary relations: the reconstitutor as the evolutionary unit of heredity.Sophie J. Veigl, Javier Suárez & Adrian Stencel - 2022 - Synthese 200 (5):1-42.
    This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstitutor by showing the limitations of (...)
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  26.  27
    Reconstructing an incomparable organism: the Chalicothere in nineteenth and early-twentieth century palaeontology.Chris Manias - 2018 - History and Philosophy of the Life Sciences 40 (1):22.
    Palaeontology developed as a field dependent upon comparison. Not only did reconstructing the fragmentary records of fossil organisms and placing them within taxonomic systems and evolutionary lineages require detailed anatomical comparisons with living and fossil animals, but the field also required thinking in terms of behavioural, biological and ecological analogies with modern organisms to understand how prehistoric animals lived and behaved. Yet palaeontological material often worked against making easy linkages, bringing a sense of mystery and doubt. This paper will look (...)
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  27.  30
    Lingüística de interações moleculares.Romeu Cardoso Guimarães - 1991 - Trans/Form/Ação 14:123-137.
    The most interesting biological molecules are long polymers. In analogy with human alphabetic languages, they can be called texts and analysed, as to the primary structure, as sequences of letters or of words . It is considered that the study of words, in a linguistic approach, may contribute positively to the understanding of molecular interactions . The molecular and human languages and dialects are contrasted. The molecular one is peculiarly distinct from the human, for instance, by its use of a (...)
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  28. Made by each other: Organisms and their environment. [REVIEW]Kim Sterelny - 2005 - Biology and Philosophy 20 (1):21-36.
    The standard picture of evolution, is externalist: a causal arrow runs from environment to organism, and that arrow explains why organisms are as they are (Godfrey-Smith 1996). Natural selection allows a lineage to accommodate itself to the specifics of its environment. As the interior of Australia became hotter and drier, phenotypes changed in many lineages of plants and animals, so that those organisms came to suit the new conditions under which they lived. Odling-Smee, Laland and Feldman, building on the (...)
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  29.  26
    The hierarchical basis of serial homology and evolutionary novelty.James DiFrisco, Alan Love & G. P. Wagner - 2023 - Journal of Morphology 284 (1):e21531.
    Given the pervasiveness of gene sharing in evolution and the extent of homology across the tree of life, why is everything not homologous with everything else? The continuity and overlapping genetic contributions to diverse traits across lineages seem to imply that no discrete determination of homology is possible. Although some argue that the widespread overlap in parts and processes should be acknowledged as “partial” homology, this threatens a broad base of presumed comparative morphological knowledge accepted by most biologists. Following a (...)
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  30.  11
    A General Model of and Lineage-Specific Ground Plans for Animal Consciousness.Daichi G. Suzuki - 2022 - Annals of the Japan Association for Philosophy of Science 31:5-29.
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  31. There Are No Intermediate Stages: An Organizational View on Development.Leonardo Bich & Derek Skillings - 2023 - In Matteo Mossio (ed.), Organization in Biology. Springer. pp. 241-262.
    Theoretical accounts of development exhibit several internal tensions and face multiple challenges. They span from the problem of the identification of the temporal boundaries of development (beginning and end) to the characterization of the distinctive type of change involved compared to other biological processes. They include questions such as the role to ascribe to the environment or what types of biological systems can undergo development and whether they should include colonies or even ecosystems. In this chapter we discuss these conceptual (...)
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  32.  52
    Lineage Explanations: Explaining How Biological Mechanisms Change.Brett Calcott - 2009 - British Journal for the Philosophy of Science 60 (1):51-78.
    This paper describes a pattern of explanation prevalent in the biological sciences that I call a ‘lineage explanation’. The aim of these explanations is to make plausible certain trajectories of change through phenotypic space. They do this by laying out a series of stages, where each stage shows how some mechanism worked, and the differences between each adjacent stage demonstrates how one mechanism, through minor modifications, could be changed into another. These explanations are important, for though it is widely (...)
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  33.  16
    Transparent things: Cell fates and cell movements during early embryogenesis of zebrafish.Lilianna Solnica-Krezel, Derek L. Stemple & Wolfgang Driever - 1995 - Bioessays 17 (11):931-939.
    Development of an animal embryo involves the coordination of cell divisions, a variety of inductive interactions and extensive cellular rearrangements. One of the biggest challenges in developmental biology is to explain the relationships between these processes and the mechanisms that regulate them. Teleost embryos provide an ideal subject for the study of these issues. Their optical lucidity combined with modern techniques for the marking and observation of individual living cells allow high resolution investigations of specific morphogenetic movements and (...)
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  34. Biological Information, Causality and Specificity - an Intimate Relationship.Karola Stotz & Paul E. Griffiths - 2017 - In Sara Imari Walker, Paul C. W. Davies & George F. R. Ellis (eds.), From Matter to Life: Information and Causality. Cambridge University Press. pp. 366-390.
    In this chapter we examine the relationship between biological information, the key biological concept of specificity, and recent philosophical work on causation. We begin by showing how talk of information in the molecular biosciences grew out of efforts to understand the sources of biological specificity. We then introduce the idea of ‘causal specificity’ from recent work on causation in philosophy, and our own, information theoretic measure of causal specificity. Biological specificity, we argue, is simple the causal specificity of certain biological (...)
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  35.  10
    Competent steps in determination of cell fate.Robert Wilson - 1999 - Bioessays 21 (6):455-458.
    Competence is an active state that defines the way in which cells respond to an inductive signal. A challenge of developmental biology is to explain not just the nature of the signalling molecules that promote cell specification or differentiation, but also how cells acquire competence to respond to these signals and what that reflects in molecular terms. A recent paper by Carmena et al.(1) has revealed how several signalling mechanisms are used sequentially and in specific combinations to specify (...)
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  36.  11
    Biological Pathway Specificity in the Cell—Does Molecular Diversity Matter?Nils G. Walter - 2019 - Bioessays 41 (8):1800244.
    Biology arises from the crowded molecular environment of the cell, rendering it a challenge to understand biological pathways based on the reductionist, low‐concentration in vitro conditions generally employed for mechanistic studies. Recent evidence suggests that low‐affinity interactions between cellular biopolymers abound, with still poorly defined effects on the complex interaction networks that lead to the emergent properties and plasticity of life. Mass‐action considerations are used here to underscore that the sheer number of weak interactions expected from the complex mixture (...)
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  37. Paleolithic public goods games: Why human culture and cooperation did not evolve in one step.Benoît Dubreuil - 2010 - Biology and Philosophy 25 (1):53-73.
    It is widely agreed that humans have specific abilities for cooperation and culture that evolved since their split with their last common ancestor with chimpanzees. Many uncertainties remain, however, about the exact moment in the human lineage when these abilities evolved. This article argues that cooperation and culture did not evolve in one step in the human lineage and that the capacity to stick to long-term and risky cooperative arrangements evolved before properly modern culture. I present evidence (...)
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  38.  43
    Why coelacanths are not 'living fossils'.Didier Casane & Patrick Laurenti - 2013 - Bioessays 35 (4):332-338.
    A series of recent studies on extant coelacanths has emphasised the slow rate of molecular and morphological evolution in these species. These studies were based on the assumption that a coelacanth is a ‘living fossil’ that has shown little morphological change since the Devonian, and they proposed a causal link between low molecular evolutionary rate and morphological stasis. Here, we have examined the available molecular and morphological data and show that: (i) low intra-specific molecular diversity does not imply low (...)
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  39.  25
    Historical resonances of the DSM-5 dispute: American exceptionalism or Eurocentrism?David Pilgrim - 2014 - History of the Human Sciences 27 (2):97-117.
    This article begins with arguments evident at the time of writing about the 5th revision of the Diagnostic and Statistical Manual of the American Psychiatric Association. The historical lineages of those arguments are international and not limited to the USA. The concern with psychiatric diagnosis both internationally and in the USA came to the fore at the end of the Second World War with the construction of the American Psychiatric Association’s Diagnostic and Statistical Manual and the World Health Organization’s classification (...)
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  40.  15
    Towards a molecular understanding of differentiation mechanisms in ascidian embryos.Noriyuki Satoh - 1987 - Bioessays 7 (2):51-56.
    The ascidian embryo has long provided a model system for ‘mosaic’ development. This article reviews recent advances in the study of ascidian developmental biology. These include: (a) the re‐analysis of cell lineages in ascidian embryos with the ascertainment of developmental fates of every blastomere of a 110‐cell embryo; (b) the development of several tissue‐specific monoclonal antibodies; (c) the investigation and description of cell cycle requirements for differentiation; it has been found that neither cytokinesis nor nuclear division is required (...)
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  41.  32
    Vacher de Lapouge and the Rise of Nazi Science.Jennifer Michael Hecht - 2000 - Journal of the History of Ideas 61 (2):285-304.
    In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Ideas 61.2 (2000) 285-304 [Access article in PDF] Vacher de Lapouge and the Rise of Nazi Science Jennifer Michael Hecht * In the literature on the history of the Shoah the existence of a tradition of explicit anti-morality has been generally ignored. 1 This article argues that the materialist anthropology of the late nineteenth and early twentieth centuries waged a direct attack on morality, (...)
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  42. An improved ontological representation of dendritic cells as a paradigm for all cell types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop (...)
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  43.  16
    Mirror mechanism and dedicated circuits are the scaffold for mirroring processes.Leonardo Fogassi - 2014 - Behavioral and Brain Sciences 37 (2):199-199.
    In the past decade many studies have demonstrated the existence of a mirror mechanism that matches the sensory representation of a biological stimulus with its somatomotor and visceromotor representation. This mechanism, likely phylogenetically very old, explains several types of mirroring behaviours, at different levels of complexity. The presence in primates of dedicated neuroanatomical pathways for specific sensorimotor integrations processes implies, at least in the primate lineage, a hard-wired mirror mechanism for social cognitive functions.
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  44.  46
    Minimal memetics and the Evolution of Patented Technology.Mark A. Bedau - 2013 - Foundations of Science 18 (4):791-807.
    The nature and status of cultural evolution and its connection with biological evolution are controversial in part because of Richard Dawkin’s suggestion that the scientific study of culture should include “memetics,” an analog of genetics in which genes are replaced by “memes”—the hypothetical units of cultural evolution. Memetics takes different forms; I focus on its minimal form, which claims merely that natural selection shapes to some extent the evolution of some aspects of culture. Advocates and critics of memetics disagree about (...)
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  45.  11
    Wild, Native, or Pure: Trout as Genetic Bodies.Christine Biermann & David G. Havlick - 2021 - Science, Technology, and Human Values 46 (6):1201-1229.
    Advances in genetics and genomics have raised new questions in trout restoration and management, specifically about species identity and purity, which fish to value, and where these fish belong. This paper examines how this molecular turn in fisheries management is influencing wild and native trout policy in Colorado. Examples from two small Colorado watersheds, Bear Creek and Sand Creek, illustrate how framing trout as genetic bodies can guide managers to care for or kill trout populations in the interest of rectifying (...)
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  46.  95
    Mechanistic Constraints on Evolutionary Outcomes.Tudor M. Baetu - 2012 - Philosophy of Science 79 (2):276-294.
    Understanding the role mechanistic constraints play in shaping evolution can relieve the tension between the generally accepted intuition that there are no strict laws in biology and empirical findings showing that evolutionary processes are biased toward preferred outcomes. Mechanistic constraints explain why some evolutionary outcomes are more probable than others and allow for predictions in specific lineages. At the same time, mechanistic constraints are neither necessary nor universal in the way laws are traditionally characterized: they remain contingent on (...)
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  47.  3
    Competent steps in determination of cell fate.Rachel Brewster & Nadia Dahmane - 1999 - Bioessays 21 (6):455-458.
    Competence is an active state that defines the way in which cells respond to an inductive signal. A challenge of developmental biology is to explain not just the nature of the signalling molecules that promote cell specification or differentiation, but also how cells acquire competence to respond to these signals and what that reflects in molecular terms. A recent paper by Carmena et al.(1) has revealed how several signalling mechanisms are used sequentially and in specific combinations to specify (...)
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  48.  11
    The chromatin domain as a unit of gene regulation.Michael A. Goldman - 1988 - Bioessays 9 (2-3):50-55.
    The process by which the genetically identical cell lineages of a multicellular organism acquire the propensity to express distinct arrays of gene products is among the most significant and fascinating questions in modern biology. Not surprisingly, this complex process requires control at several levels, each level providing a condition that is necessary but not sufficient for transcription to occur. Evidence suggests that one level of control concerns a region of DNA much larger than the transcription unit itself – the (...)
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  49.  17
    Analysis of development and differentiation with tumour cell glycoproteins.Gordon Koch & Michael Smith - 1985 - Bioessays 3 (5):196-199.
    The repertoire of acceptor glycoproteins for concanavalin A expressed by a cultured tumour cell reflects the normal developmental lineage from which it was derived, as well as the degree of maturation along that lineage. Antibodies to this particular set of glycoproteins show a considerable specificity towards normal differentiation antigens which are often preferentially associated with the less mature intermediates of the corresponding pathway. In addition, comparisons between ‘immature’ and ‘mature’ tumour cells can be used to identify glycoproteins associated (...)
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  50.  10
    Cytoskeletal diversification across 1 billion years: What red algae can teach us about the cytoskeleton, and vice versa.Holly V. Goodson, Joshua B. Kelley & Susan H. Brawley - 2021 - Bioessays 43 (5):2000278.
    The cytoskeleton has a central role in eukaryotic biology, enabling cells to organize internally, polarize, and translocate. Studying cytoskeletal machinery across the tree of life can identify common elements, illuminate fundamental mechanisms, and provide insight into processes specific to less‐characterized organisms. Red algae represent an ancient lineage that is diverse, ecologically significant, and biomedically relevant. Recent genomic analysis shows that red algae have a surprising paucity of cytoskeletal elements, particularly molecular motors. Here, we review the genomic and (...)
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