Inferential explanations in biology

Among philosophers of science, there is now a widespread agreement that the DN model of explanation is poorly equipped to account for explanations in biology. Rather than identifying laws, so the consensus goes, researchers explain biological capacities by constructing a model of the underlying mechanism.We think that the dichotomy between DN explanations and mechanistic explanations is misleading. In this article, we argue that there are cases in which biological capacities are explained without constructing a model of the underlying mechanism. Although these explanations do not conform to Hempel’s DN model (they do not deduce the explanandum from laws of nature), they do invoke more or less stable generalisations. Because they invoke generalisations and have the form of an argument, we call them inferential explanations. We support this claim by considering two examples of explanations of biological capacities: pigeon navigation and photoperiodism. Next, we will argue that these non-mechanistic explanations are crucial to biology in three ways: (i) sometimes, they are the only thing we have (there is no alternative available), (ii) they are heuristically useful, and (iii) they provide genuine understanding and so are interesting in their own right.In the last sections we discuss the relation between types of explanations and types of experiments and situate our views within some relevant debates on explanatory power and explanatory virtues.     

Recent applications of Hidden Markov Models in computational biology

This paper examines recent developments and applications of Hidden Markov Models (HMMs) to various problems in computational biology, including multiple sequence alignment, homology detection, protein sequences classification, and genomic annotation.     

Recent progress in auxin biology

Like animals, plants have evolved into complex organisms. Developmental cohesion between tissues and cells is possible due to signaling molecules (messengers) like hormones. The first hormone discovered in plants was auxin. This phytohormone was first noticed because of its involvement in the response to directional light. Nowadays, auxin has been established as a central key player in the regulation of plant growth and development and in responses to environmental changes. At the cellular level, auxin controls division, elongation, and differentiation as well as the polarity of the cell. Auxin, to integrate so many different signals, needs to be regulated at many different levels. A tight regulation of auxin synthesis, activity, degradation as well as transport has been demonstrated. Another possibility to modulate auxin signaling is to modify the capacity of response of the cells by expressing differentially the signaling components. In this review, we provide an overview of the present knowledge in auxin biology, with emphasis on root development.     

New opportunities by synthetic biology for biopharmaceutical production in Pichia pastoris

1. Download : Download high-res image (260KB)
2. Download : Download full-size image

Highlights► The application of Pichia pastoris for biopharmaceutical production is described. ► Synthetic biology approaches and perspectives to improve production are reviewed. ► Glycoengineering efforts to produce humanized, uniform glycoproteins are covered. ► The design and application of synthetic promoter variants are highlighted. ► The molecular toolbox available for synthetic biology in P. pastoris is discussed.     

A role for immunology in invasion biology

Invasive species are of increasing conservation and economic concern, yet mechanisms underlying invasions remain poorly understood. We propose that variation in immune defences might help explain why only some introduced populations become invasive. Introduced species escape many of their native diseases, but also face novel pathogens that can induce costly, and sometimes deadly, immune responses in na?ve hosts. Therefore, favouring less resource-demanding and dangerous defence mechanisms and allocating a greater proportion of resources to growth and reproduction should favour invasion. Specifically, we argue that successful invaders should reduce costly systemic inflammatory responses, which are associated with fever and metabolic and behavioural changes, and rely more heavily on less expensive antibody-mediated immunity. Here we provide supporting arguments for this hypothesis and generate predictions that are testable using tools from the growing field of ecological immunology.     

糖尿病肾病动物模型的研究进展

糖尿病肾病是终末期肾衰的主要原因,也是糖尿病致命的重要原因。但是糖尿病肾病的致病机制迄今尚不完全明了,理想的动物模型无疑可对糖尿病肾病的研究提供重要线索。糖尿病肾病动物模型包括诱发性、自发性和转基因等多种类型的动物模型,各种类型的动物模型在疾病的发生发展、病理生理变化等多个方面与人类糖尿病肾病具有相似的特征。应用这些模型有助于开展对糖尿病肾病的防治、发病机理、相关药物的开发等多方面的研究。     

Shifting to structures in physics and biology: a prophylactic for promiscuous realism

Within the philosophy of science, the realism debate has been revitalised by the development of forms of structural realism. These urge a shift in focus from the object oriented ontologies that come and go through the history of science to the structures that remain through theory change. Such views have typically been elaborated in the context of theories of physics and are motivated by, first of all, the presence within such theories of mathematical equations that allow straightforward representation of the relevant structures; and secondly, the implications of such theories for the individuality and identity of putative objects. My aim in this paper is to explore the possibility of extending such views to biological theories. An obvious concern is that within the context of the latter it is typically insisted that we cannot find the kinds of highly mathematised structures that structural realism can point to in physics. I shall indicate how the model-theoretic approach to theories might help allay such concerns. Furthermore, issues of identity and individuality also arise within biology. Thus Dupré has recently noted that there exists a 'General Problem of Biological Individuality' which relates to the issue of how one divides 'massively integrated and interconnected' systems into discrete components. In response Dupré advocates a form of 'Promiscuous Realism' that holds, for example, that there is no unique way of dividing the phylogenetic tree into kinds. Instead I shall urge serious consideration of those aspects of the work of Dupré and others that lean towards a structuralist interpretation. By doing so I hope to suggest possible ways in which a structuralist stance might be extended to biology.     

Engaging students in constructing scientific explanations in biology classrooms: a lesson-design model

Abstract

Constructing scientific explanations of natural phenomena is an important aim of science education. Explanation oriented science teaching approaches encourage learners to engage in sense-making discussions and construct the causal accounts of the phenomena under study. This article demonstrates a lesson-design model that guides biology teachers on how to integrate explanation oriented teaching in their everyday practice. The proposed model includes six phases: (1) presenting a hooking activity; (2) formulating a how-why type focus question; (3) constructing the initial causal story; (4) using authentic data, scientific facts, principles, and disciplinary core ideas to revise-refine the causal story; (5) discussing-rewriting the refined causal story; (6) applying the causal-mechanistic knowledge in a new context or problem scenario. An eleventh-grade lesson on the topic ‘protein biosynthesis in cells’ serves an example about how this model can be operationalized to design and implement explanation oriented biology lessons.     

Recent endeavors on molecular imaging for mapping metals in biology

Transition metals such as zinc,copper and iron play vital roles in maintaining physiological functions and homeostasis of living systems.Molecular imaging inclu...     

Plasmodium development in the mosquito: biology bottlenecks and opportunities for mathematical modeling

Quantitative analyses of malaria parasite development are necessary to assess the efficacy of control measures. Such analyses in the mammalian host have been difficult to implement, lagging behind the use of antiparasitic drugs, vaccine development and transmission-blocking strategies. Even less is known about the genetic, environmental and other factors that impact sporogony in the mosquito host. Here, we summarize current knowledge and review a first attempt to model sporogonic development quantitatively.     

Acanthamoeba: biology and increasing importance in human health

Acanthamoeba is an opportunistic protozoan that is widely distributed in the environment and is well recognized to produce serious human infections, including a blinding keratitis and a fatal encephalitis. This review presents our current understanding of the burden of Acanthamoeba infections on human health, their pathogenesis and pathophysiology, and molecular mechanisms associated with the disease, as well as virulence traits of Acanthamoeba that may be targets for therapeutic interventions and/or the development of preventative measures.     

A role for chemistry in stem cell biology

Although stem cells hold considerable promise for the treatment of numerous diseases including cardiovascular disease, neurodegenerative disease, musculoskeletal disease, diabetes and cancer, obstacles such as the control of stem cell fate, allogenic rejection and limited cell availability must be overcome before their therapeutic potential can be realized. This requires an improved understanding of the signaling pathways that affect stem cell fate. Cell-based phenotypic and pathway-specific screens of natural products and synthetic compounds have recently provided a number of small molecules that can be used to selectively control stem cell proliferation and differentiation. Examples include the selective induction of neurogenesis and cardiomyogenesis in murine embryonic stem cells, osteogenesis in mesenchymal stem cells and dedifferentiation in skeletal muscle cells. Such molecules will likely provide new insights into stem cell biology, and may ultimately contribute to effective medicines for tissue repair and regeneration.     

The role of theory in an emerging new plant reproductive biology

Recent empirical studies hint at an end to the historical solitude between pollination and mating system approaches to plant reproductive character evolution. Now is an opportune time to distill theoretical results into comprehensible insight, and to integrate these findings into the emerging new plant reproductive biology. We outline four theoretical insights for understanding the evolution of reproductive characters, and show how these allow researchers to dissect complex ecological scenarios into clear and evolutionarily relevant components.     

New tools and new biology: Recent miniaturized systems for molecular and cellular biology

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology.     

类风湿性关节炎啮齿动物模型的研究进展

类风湿性关节炎是一种常见的致残性疾病之一,病因未明。研究此类疾病的有效方法是建立、研究并应用动物模型。通过对目前国内外类风湿性关节炎模型复制方法、机制和应用的研究,分析各自的特点及不足之处,提出复制更加符合类风湿性关节炎临床特点的动物模型的展望与设想。     

Recent initiatives for radiation oncology resident education in radiation and cancer biology

Nearly all residents from accredited radiation oncology residency programs in the United States are required to take the American College of Radiology (ACR) In-Training examination each year. The test is comprised of three sections: Clinical Radiation Oncology, Radiological Physics, and Radiation (and Cancer) Biology. Here we provide an update on changes to the biology portion of the ACR exam. We also discuss the availability and use of the ACR and biology practice exams as assessment and teaching tools for both the instructors of radiation and cancer biology and the residents they teach.     

A role for SHIP in stem cell biology and transplantation

Inositol phospholipid signaling pathways have begun to emerge as important players in stem cell biology and bone marrow transplantation [1-4]. The SH2-containing Inositol Phosphatase (SHIP) is among the enzymes that can modify endogenous mammalian phosphoinositides. SHIP encodes an isoform specific to pluripotent stem (PS) cells [5,6] plays a role in hematopoietic stem (HS) cell biology [7,8] and allogeneic bone marrow (BM) transplantation [1,2,9,10]. Here I discuss our current understanding of the cell and molecular pathways that SHIP regulates that influence PS/HS cell biology and BM transplantation. Genetic models of SHIP-deficiency indicate this enzyme is a potential molecular target to enhance both autologous and allogeneic BM transplantation. Thus, strategies to reversibly target SHIP expression and their potential application to stem cell therapies and allogeneic BMT are also discussed.