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The Problem of Emergence

John F. Padgett and Walter W. Powell

in The Emergence of Organizations and Markets

This chapter elaborates on a theory of the co-evolution of social networks—a synthesis of social science and biochemistry—and shows its empirical significance for the study of human organizations. ... More

This chapter elaborates on a theory of the co-evolution of social networks—a synthesis of social science and biochemistry—and shows its empirical significance for the study of human organizations. First, the chapter describes the problem of organizational novelty in the context of multiple social networks. Second, the core dynamic motor of autocatalysis both at the level of chemical and economic production and at the level of the biographical production of persons through interactive learning, communication, and teaching is explained. Third, the chapter describes eight network mechanisms of organizational genesis that have been discovered in this volume's case studies. Finally, it points to the important outstanding issue of structural vulnerability to tipping.Less

Autocatalysis in Chemistry and the Origin of Life

John F. Padgett

in The Emergence of Organizations and Markets

This chapter provides an extensive review of the biochemistry literature on the origins of life where the concept of autocatalysis figures most prominently. There is a lively debate in the scientific ... More

This chapter provides an extensive review of the biochemistry literature on the origins of life where the concept of autocatalysis figures most prominently. There is a lively debate in the scientific literature between scientists who subscribe to an RNA-first hypothesis and scientists who subscribe to a metabolism-first hypothesis about the origin of life. Both are different versions of autocatalysis, and a sensible conclusion could be that biological life really took off when a symbiosis developed between the two. After that, the chapter reviews past formal modeling in this area, which is spotty but highly suggestive. The chapter identifies Eigen's and Schuster's model of hypercycles as the path-breaking work that first placed empirical chemistry and formal models into fruitful dialogue with each other. Finally, the chapter reviews a less successful, more philosophical descendant of autocatalysis called autopoiesis, which is the guise under which autocatalysis first was presented to social scientists.Less

Tessellations

Pierre Calka

in New Perspectives in Stochastic Geometry

Random tessellations and cellular structures occur in many domains of application, such as astrophysics, ecology, telecommunications, biochemistry and naturally cellular biology (see Stoyan, Kendall ... More

Random tessellations and cellular structures occur in many domains of application, such as astrophysics, ecology, telecommunications, biochemistry and naturally cellular biology (see Stoyan, Kendall and Mecke 1987 or Okabe, Boots, Sugihara and Chiu 2000 for complete surveys). The theoretical study of these objects was initiated in the second half of the twentieth century by D. G. Kendall, J. L. Meijering, E. N. Gilbert and R. E. Miles, notably. Two isotropic and stationary models have emerged as the most basic and useful: the Poisson hyperplane tessellation and the Poisson–Voronoi tessellation. Since then, a large majority of questions raised about random tessellations have concerned statistics of the population of cells (‘how many cells are triangles in the plane?’, ‘how many cells have a volume greater than one?’) or properties of a specific cell (typically the one containing the origin). Two types of results are presented below: exact distributional calculations and asymptotic estimations. In the first part, we describe the two basic constructions of random tessellations (i.e. by throwing random hyperplanes or by constructing Voronoi cells around random nuclei) and we introduce the fundamental notion of typical cell of a stationary tessellation. The second part is devoted to the presentation of exact distributional results on basic geometrical characteristics (number of hyperfaces, typical k‐face, etc.). The following part concerns asymptotic properties of the cells. It concentrates in particular on the well‐known D. G. Kendall conjecture which states that large planar cells in a Poisson line tessellation are close to the circular shape. In the last part, we present some recent models of iterated tessellations which appear naturally in applied fields (study of crack structures, telecommunications). Intentionally, this chapter does not contain an exhaustive presentation of all the models of random tessellations existing in the literature (in particular, dynamical constructions such as Johnson‐Mehl tessellations will be omitted). The aim of the text below is to provide a selective view of recent selected methods and results on a few specific models.Less

Against Reductionism

E. Brian Davies

in Science in the Looking Glass: What Do Scientists Really Know?

The extraordinary development of physical science over the last two centuries has led to claims that it can explain all aspects of reality. Some scientists have proposed a programme called ... More

The extraordinary development of physical science over the last two centuries has led to claims that it can explain all aspects of reality. Some scientists have proposed a programme called (scientific) reductionism, describing how this is to be achieved. This chapter argues that the world is too complex and inter-related for an explanation of everything to be possible. (‘possible’ means possible in fact, not possible in principle). Application of the reductionist method to biochemistry and cell physiology, money, information and complexity, and subjective consciousness are discussed.Less

The functional neuroanatomy of learning and memory

Hans J. Markowitsch and Martina Piefke

in The Handbook of Clinical Neuropsychology

This chapter describes the kinds of learning and memory which are relevant for clinical practice and how they are defined and delineated. Two main lines are followed: one which divides information ... More

This chapter describes the kinds of learning and memory which are relevant for clinical practice and how they are defined and delineated. Two main lines are followed: one which divides information processing with respect to time, and another with respect to contents. It addresses questions concerning how information is transmitted in the brain (encoded, stored, or represented), and how information is retrieved. It describes the anatomical circuits and networks engaged in these processes with references made to the brain's biochemistry (transmitters, hormones), as far as it is relevant for learning and memory, and such disorders.Less

Introduction

David J. Price and David J. Willshaw

in Mechanisms of Cortical Development

Life on Earth began several billion years ago. The cerebral cortex of mammals probably arose from the primordial cortex of amphibians and reptiles some 300 million years ago. The evolution of the ... More

Life on Earth began several billion years ago. The cerebral cortex of mammals probably arose from the primordial cortex of amphibians and reptiles some 300 million years ago. The evolution of the mammalian brain has involved the disproportionate enlargement of the cortex and, in particular, the rapid development of the neocortex. This book explains what is known about the fundamental mechanisms that underlie the development of the neocortex of mammals, drawing on supporting evidence from other species, particularly other vertebrates. The developmental biology of cortical cells and the morphology of the structures that they form is interwoven with a detailed account of their biochemistry and the genetic origin of the factors that are thought to control key developmental processes. While the primary account of the development of the neocortex necessarily is of the results of experimental neuroscience, where appropriate the results are interpreted on the basis of the various formal models that have been proposed. Understanding the mechanisms of cortical development will have a great impact on our ability to comprehend and treat neurological diseases.Less

Guidance of axons and innervation of cortical structures

David J. Price and David J. Willshaw

in Mechanisms of Cortical Development

To create the nervous system, precise synaptic connections must form between cells. This process involves the outgrowth of axons, their travel to distant sites, and their innervation of target ... More

To create the nervous system, precise synaptic connections must form between cells. This process involves the outgrowth of axons, their travel to distant sites, and their innervation of target structures. Axons travel together in discrete bundles, which in the adult can be several centimetres long. However, at the time of axonal outgrowth the distances to be travelled are very much shorter than this. There is a range of possible types of mechanism which can yield guidance with differing degrees of precision. This chapter examines the mechanisms for axon guidance, cortical connections in the adult brain, observations on the development of cortical connections, geniculocortical development, corticofugal and corticocortical systems, mechanisms controlling the development of axonal connections, the biochemistry of growth cones, genetic analysis of axonal guidance in non-mammalian species, and mechanisms of axonal guidance in the cerebral cortex.Less

The Role of Biochemistry

Rowland H. Davis

in The Microbial Models of Molecular Biology: From Genes to Genomes

This chapter takes up three important areas in which continuing progress in molecular biology relied heavily on frankly biochemical orientation. It argues that the often understated contributions of ... More

This chapter takes up three important areas in which continuing progress in molecular biology relied heavily on frankly biochemical orientation. It argues that the often understated contributions of biochemistry to molecular biology were actually substantial and in many cases indispensable to rapid progress. Many historians point only to the discovery of DNA as they extend their accounts from a brief mention of biochemical genetics. The nature and replication of phage could not have been appreciated without early biochemical characterizations. And the Central Dogma would have remained a poorly examined dogma indeed had it not gained the flesh that orthodox biochemists put on it between 1955 and 1965.Less

Intensive Care

Caroline Whymark, Ross Junkin, and Judith Ramsey

in SBAs for the Final FRCA

Ancient DNA

Noreen Tuross and Michael G. Campana

in The Science of Roman History: Biology, Climate, and the Future of the Past

This chapter examines how ancient DNA (aDNA) analysis has helped reconstruct ancient history. It focuses in particular on cases investigating Roman history. History leaves traces in the human genome ... More

This chapter examines how ancient DNA (aDNA) analysis has helped reconstruct ancient history. It focuses in particular on cases investigating Roman history. History leaves traces in the human genome as well as those of pathogens and domesticates. While much can be gleaned from the genetic fossils preserved in extant genomes, genomes are palimpsests, with more recent events overwriting previous ones in part. The study of aDNA—DNA preserved in archaeological, paleontological, and museum sources—permits investigations into the genome before and after historic events and observations into how it evolves in real time. The field of aDNA also has a palimpsestic nature in which older results are not only extended and revised, but totally discarded due to rapid technological advances. The chapter briefly describes biochemistry of ancient DNA and the history of its research. Through several key case studies, it shows the potential for aDNA research to clarify the course of ancient history, and also highlights some of its weaknesses and limitations.Less

The biochemical basis of migraine predisposition

Vivette Glover and Merton Sandler

in Migraine: A Spectrum of Ideas

This chapter discusses some aspects of the biochemistry of migraine predisposition, and indicate how some of the initiating factors may interact with the central monoamine systems. Professor Lance ... More

This chapter discusses some aspects of the biochemistry of migraine predisposition, and indicate how some of the initiating factors may interact with the central monoamine systems. Professor Lance and others have discussed persuasively how these centres (particularly the raphe nuclei and locus coeruleus) may be involved in the generation of a migraine attack. It is likely that the more we understand about individual vulnerability, the more we may be able to tailor specific treatment to particular patients.Less

Rolling the Dice Twice: Evolving Reconstructed Ancient Proteins in Extant Organisms

Betul Kacar

in Chance in Evolution

Scientists have access to artifacts of evolutionary history, but they have limited ability to infer the exact events that produced today’s living world. An intriguing question to arise from this ... More

Scientists have access to artifacts of evolutionary history, but they have limited ability to infer the exact events that produced today’s living world. An intriguing question to arise from this limitation is whether the evolutionary paths of organisms are dominated by controlled processes, or whether they are inherently random, subject to different outcomes if repeated. Two experimental approaches, ancestral sequence reconstruction and experimental evolution, can be used to recapitulate ancient adaptive pathways and provide insights into the mutational steps that constitute an organism’s genetic heritage. Ancestral sequence reconstruction follows a backwards-from-present-day strategy in which ancestral forms of a gene or protein are reconstructed and studied mechanistically. Experimental evolution, by contrast, follows a forward-from-present-day strategy in which microbial populations are evolved in the laboratory under defined conditions. Here I describe a novel hybrid of these two methods, in which synthetic components constructed from inferred ancestral gene or protein sequences are placed into the genomes of modern organisms that are then experimentally evolved. Through this system, we aim to establish the comparative study of ancient phenotypes as a novel, statistically rigorous methodology with which to explore the impacts of biophysics and chance in evolution within the scope of the Extended Synthesis.Less

The Professional Schools

Morton Keller and Phyllis Keller

in Making Harvard Modern: The Rise of America's University

Harvard’s nine professional schools were on the cutting edge of its evolution from a Brahmin to a meritocratic university. Custom, tradition, and the ... More

Harvard’s nine professional schools were on the cutting edge of its evolution from a Brahmin to a meritocratic university. Custom, tradition, and the evergreen memory of the alumni weighed less heavily on them than on the College. And the professions they served were more interested in their current quality than their past glory. True, major differences of size, standing, wealth, and academic clout separated Harvard’s Brobdingnagian professional faculties—the Graduate School of Arts and Sciences and the Schools of Medicine, Law, and Business— from the smaller, weaker Lilliputs—Public Health and Dentistry, Divinity, Education, Design, Public Administration. But these schools had a shared goal of professional training that ultimately gave them more in common with one another than with the College and made them the closest approximation of Conant’s meritocratic ideal. Harvard’s doctoral programs in the Graduate School of Arts and Sciences (GSAS) were a major source of its claim to academic preeminence. As the Faculty of Arts and Sciences became more research and discipline minded, so grew the importance of graduate education. A 1937 ranking of graduate programs in twenty-eight fields—the lower the total score, the higher the overall standing—provided a satisfying measure of Harvard’s place in the American university pecking order: But there were problems. Money was short, and while graduate student enrollment held up during the Depression years of the early 1930s (what else was there for a young college graduate to do?), academic jobs became rare indeed. Between 1926–27 and 1935–36, Yale appointed no Harvard Ph.D. to a junior position. The Graduate School itself was little more than a degree-granting instrument, with no power to appoint faculty, no building, no endowment, and no budget beyond one for its modest administrative costs. Graduate students identified with their departments, not the Graduate School. Needless to say, the GSAS deanship did not attract the University’s ablest men. Conant in 1941 appointed a committee to look into graduate education, and historian Arthur M. Schlesinger, Sr., “called for a thoroughgoing study without blinders. Less

Mathematical Chemistry, a New Discipline

Guillermo Restrepo

in Essays in the Philosophy of Chemistry

THE AIM OF THIS chapter is to ponder and discuss the relationship between chemistry and mathematics, taking into account some early research we have ... More

THE AIM OF THIS chapter is to ponder and discuss the relationship between chemistry and mathematics, taking into account some early research we have performed on the subject (Restrepo and Schummer 2014; Restrepo and Villaveces 2012, 2013; Restrepo 2013). In those works we have discussed some criticism and some support throughout history regarding the relationship. We analyzed the opinions of scholars ranging from Venel and Denis Diderot (eighteenth century) to Pierre Laszlo (twentieth century), all of whom are critical of mathematical chemistry. We also analyzed opinions by Brown and Paul Dirac (nineteenth and twentieth centuries, respectively), who sought a fruitful relationship between mathematics and chemistry. We discussed Kant and his double opinion regarding such a relationship as well. (In summary, Kant initially did not consider chemistry to be a science because of its apparent lack of mathematization, an idea Kant supported in the apparent a priori background of mathematics and in the a posteriori one of chemistry. Kant’s revised opinion about the relationship between mathematics and chemistry is totally different, Kant now thinks chemistry contains elements of mathematics.) We have also analyzed Comte’s opinions on the necessity of mathematics for chemistry and for the advancement of the latter (Restrepo 2013). Our work on the philosophy and history of the relationship between mathematics and chemistry is driven by the attention research on the field has gained between the 1960s and the present. A wealth of knowledge in the border between the two sciences has been generated but little attention has been paid to the philosophy and history of the subject (Restrepo and Schummer 2012). Thus in recent years scholars (Balaban 2005, 2013; Basak 2013; Deltete 2012; Gavroglu and Simões 2012; Restrepo and Villaveces 2012, 2013; Restrepo 2013; Schummer 2012; Hosoya 2013; Klein 2013), including the author of the present chapter, have decided to study such a relationship from both a historical and a philosophical viewpoint. One example of the increased interest are the special issues of Hyle, which were dedicated to mathematical chemistry. Less