2,707 research outputs found

    Concepts of Drift and Selection in “The Great Snail Debate” of the 1950s and Early 1960s

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    Recently, much philosophical discussion has centered on the best way to characterize the concepts of random drift and natural selection, and, in particular, on the question of whether selection and drift can be conceptually distinguished (Beatty 1984; Brandon 2005; Hodge 1983, 1987; Millstein 2002, 2005; Pfeifer 2005; Shanahan 1992; Stephens 2004). These authors all contend, to a greater or lesser degree, that their concepts make sense of biological practice. So, it should be instructive to see how the concepts of drift and selection were distinguished by the disputants in a high-profile debate; debates such as these often force biologists to take a more philosophical turn, discussing the concepts at issue in greater detail than usual. A prime candidate for just such a case study is what William Provine (1986) has termed “The Great Snail Debate,” that is, the debate over the highly polymorphic land snails Cepaea nemoralis and Cepaea hortensis in the 1950s and early 1960s. This study will reveal that much of the present-day confusion over the concepts of drift and selection is rooted in confusions of the past. Nonetheless, there are lessons that can be learned about nonadaptiveness, indiscriminate sampling, and causality with respect to these two concepts. In particular, this paper will shed light on the following questions: 1) What is “drift”? Is “drift” a purely mathematical construct, a physical process analogous to the indiscriminate sampling of balls from an urn, or the outcome of a sampling process? 2) What is “nonadaptiveness,” and is a proponent of drift committed to claims that organisms’ traits are nonadaptive? 3) Can disputes concerning selection and drift be settled by statistics alone, or is causal information essential? If causal information is essential, what does that say about the concepts of “drift” and “selection” themselves

    Probabilistic Program Abstractions

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    Abstraction is a fundamental tool for reasoning about complex systems. Program abstraction has been utilized to great effect for analyzing deterministic programs. At the heart of program abstraction is the relationship between a concrete program, which is difficult to analyze, and an abstract program, which is more tractable. Program abstractions, however, are typically not probabilistic. We generalize non-deterministic program abstractions to probabilistic program abstractions by explicitly quantifying the non-deterministic choices. Our framework upgrades key definitions and properties of abstractions to the probabilistic context. We also discuss preliminary ideas for performing inference on probabilistic abstractions and general probabilistic programs

    Generating and Sampling Orbits for Lifted Probabilistic Inference

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    A key goal in the design of probabilistic inference algorithms is identifying and exploiting properties of the distribution that make inference tractable. Lifted inference algorithms identify symmetry as a property that enables efficient inference and seek to scale with the degree of symmetry of a probability model. A limitation of existing exact lifted inference techniques is that they do not apply to non-relational representations like factor graphs. In this work we provide the first example of an exact lifted inference algorithm for arbitrary discrete factor graphs. In addition we describe a lifted Markov-Chain Monte-Carlo algorithm that provably mixes rapidly in the degree of symmetry of the distribution

    Understanding Leopold’s Concept of ‘Interdependence’ for Environmental Ethics and Conservation Biology

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    Aldo Leopold’s Land Ethic, an extremely influential view in environmental ethics and conservation biology, is committed to the claim that interdependence between humans, other species, and abiotic entities plays a central role in our ethical responsibilities. Thus, a robust understanding of “interdependence” is necessary for evaluating the viability of the Land Ethic and related views, including ecological ones. I characterize and defend a Leopoldian concept of “interdependence,” arguing that it ought to include both negative and positive causal relations. I also show that strength and type of interdependence can vary with time, space, and context

    Transcriptionally inactive oocyte-type 5S RNA genes of Xenopus laevis are complexed with TFIIIA in vitro

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    An extract from whole oocytes of Xenopus laevis was shown to transcribe somatic-type 5S RNA genes approximately 100-fold more efficiently than oocyte-type 5S RNA genes. This preference was at least 10-fold greater than the preference seen upon microinjection of 5S RNA genes into oocyte nuclei or upon in vitro transcription in an oocyte nuclear extract. The approximately 100-fold transcriptional bias in favor of the somatic-type 5S RNA genes observed in vitro in the whole oocyte extract was similar to the transcriptional bias observed in developing Xenopus embryos. We also showed that in the whole oocyte extract, a promoter-binding protein required for 5S RNA gene transcription, TFIIIA, was bound both to the actively transcribed somatic-type 5S RNA gene and to the largely inactive oocyte-type 5S RNA genes. These findings suggest that the mechanism for the differential expression of 5S RNA genes during Xenopus development does not involve differential binding of TFIIIA to 5S RNA genes

    Symbolic Exact Inference for Discrete Probabilistic Programs

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    The computational burden of probabilistic inference remains a hurdle for applying probabilistic programming languages to practical problems of interest. In this work, we provide a semantic and algorithmic foundation for efficient exact inference on discrete-valued finite-domain imperative probabilistic programs. We leverage and generalize efficient inference procedures for Bayesian networks, which exploit the structure of the network to decompose the inference task, thereby avoiding full path enumeration. To do this, we first compile probabilistic programs to a symbolic representation. Then we adapt techniques from the probabilistic logic programming and artificial intelligence communities in order to perform inference on the symbolic representation. We formalize our approach, prove it sound, and experimentally validate it against existing exact and approximate inference techniques. We show that our inference approach is competitive with inference procedures specialized for Bayesian networks, thereby expanding the class of probabilistic programs that can be practically analyzed
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