William Jagust and Mark D'Esposito (eds)
- Published in print:
- 2009
- Published Online:
- February 2010
- ISBN:
- 9780195328875
- eISBN:
- 9780199864836
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195328875.001.0001
- Subject:
- Neuroscience, Techniques, Development
The study of brain aging has been revolutionized through advances in molecular neuroscience, cognitive neuroscience, and brain imaging. The application of new concepts and techniques has permitted ...
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The study of brain aging has been revolutionized through advances in molecular neuroscience, cognitive neuroscience, and brain imaging. The application of new concepts and techniques has permitted investigators to explore the changes in structure, function, and biochemistry in living humans in order to unravel mechanisms that underlie both age-related cognitive decline and preservation of cognition into old age. This book reviews both the basic science and clinical applications of brain imaging in the study of brain aging. Topics reviewed include technical issues associated with imaging studies in older brains, pathology of brain aging, structural changes in the aging brain, changes in dopamine function, and mechanisms of brain reserve and plasticity. The use of genetics in combination with brain imaging and the use of animal models are also explored. Clinical applications include the diagnosis and prediction of cognitive decline using a variety of different imaging approaches as well as a detailed description of amyloid imaging using PET scanning. Other topics include functional MRI studies in aging, the use of imaging in therapeutic monitoring and drug development, and the role of large-scale databases. The volume contains information both for those involved in brain imaging research and for those new to the field who are in need of a systematic overview.Less
The study of brain aging has been revolutionized through advances in molecular neuroscience, cognitive neuroscience, and brain imaging. The application of new concepts and techniques has permitted investigators to explore the changes in structure, function, and biochemistry in living humans in order to unravel mechanisms that underlie both age-related cognitive decline and preservation of cognition into old age. This book reviews both the basic science and clinical applications of brain imaging in the study of brain aging. Topics reviewed include technical issues associated with imaging studies in older brains, pathology of brain aging, structural changes in the aging brain, changes in dopamine function, and mechanisms of brain reserve and plasticity. The use of genetics in combination with brain imaging and the use of animal models are also explored. Clinical applications include the diagnosis and prediction of cognitive decline using a variety of different imaging approaches as well as a detailed description of amyloid imaging using PET scanning. Other topics include functional MRI studies in aging, the use of imaging in therapeutic monitoring and drug development, and the role of large-scale databases. The volume contains information both for those involved in brain imaging research and for those new to the field who are in need of a systematic overview.
John F. Padgett and Walter W. Powell
- Published in print:
- 2012
- Published Online:
- October 2017
- ISBN:
- 9780691148670
- eISBN:
- 9781400845552
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691148670.003.0001
- Subject:
- Sociology, Economic Sociology
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. ...
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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
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.
John F. Padgett
- Published in print:
- 2012
- Published Online:
- October 2017
- ISBN:
- 9780691148670
- eISBN:
- 9781400845552
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691148670.003.0002
- Subject:
- Sociology, Economic Sociology
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 ...
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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
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.
Pierre Calka
- Published in print:
- 2009
- Published Online:
- February 2010
- ISBN:
- 9780199232574
- eISBN:
- 9780191716393
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199232574.003.0005
- Subject:
- Mathematics, Geometry / Topology
Random tessellations and cellular structures occur in many domains of application, such as astrophysics, ecology, telecommunications, biochemistry and naturally cellular biology (see Stoyan, Kendall ...
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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
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.
Donald T. Stuss and Robert T. Knight (eds)
- Published in print:
- 2002
- Published Online:
- May 2009
- ISBN:
- 9780195134971
- eISBN:
- 9780199864157
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195134971.001.0001
- Subject:
- Neuroscience, Behavioral Neuroscience, Molecular and Cellular Systems
This book provides a review of historical and current research on the function of the frontal lobes and frontal systems of the brain. The content spans frontal lobe functions from birth to old age, ...
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This book provides a review of historical and current research on the function of the frontal lobes and frontal systems of the brain. The content spans frontal lobe functions from birth to old age, from biochemistry and anatomy to rehabilitation, and from normal to disrupted function. The book covers a variety of disciplines including neurology, neuroscience, psychiatry, psychology, and health care.Less
This book provides a review of historical and current research on the function of the frontal lobes and frontal systems of the brain. The content spans frontal lobe functions from birth to old age, from biochemistry and anatomy to rehabilitation, and from normal to disrupted function. The book covers a variety of disciplines including neurology, neuroscience, psychiatry, psychology, and health care.
E. Brian Davies
- Published in print:
- 2007
- Published Online:
- September 2008
- ISBN:
- 9780199219186
- eISBN:
- 9780191711695
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199219186.003.0009
- Subject:
- Physics, History of Physics
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 ...
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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 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.
Hans J. Markowitsch and Martina Piefke
- Published in print:
- 2010
- Published Online:
- September 2010
- ISBN:
- 9780199234110
- eISBN:
- 9780191594250
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199234110.003.038
- Subject:
- Psychology, Neuropsychology, Clinical Psychology
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 ...
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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
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.
David J. Price and David J. Willshaw
- Published in print:
- 2000
- Published Online:
- January 2010
- ISBN:
- 9780192624277
- eISBN:
- 9780191723735
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780192624277.003.0001
- Subject:
- Neuroscience, 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 ...
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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
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.
David J. Price and David J. Willshaw
- Published in print:
- 2000
- Published Online:
- January 2010
- ISBN:
- 9780192624277
- eISBN:
- 9780191723735
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780192624277.003.0004
- Subject:
- Neuroscience, 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 ...
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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
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.
Rowland H. Davis
- Published in print:
- 2003
- Published Online:
- April 2010
- ISBN:
- 9780195154368
- eISBN:
- 9780199893935
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195154368.003.0017
- Subject:
- Biology, Biochemistry / Molecular Biology
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 ...
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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
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.
Mathias Grote
- Published in print:
- 2019
- Published Online:
- January 2020
- ISBN:
- 9780226625157
- eISBN:
- 9780226625294
- Item type:
- book
- Publisher:
- University of Chicago Press
- DOI:
- 10.7208/chicago/9780226625294.001.0001
- Subject:
- History, History of Science, Technology, and Medicine
This book tells the story of how a molecular-mechanical vision of life has become omnipresent in the sciences, biomedicine, and bio- and nanotechnologies of the late twentieth century. Thereby, it ...
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This book tells the story of how a molecular-mechanical vision of life has become omnipresent in the sciences, biomedicine, and bio- and nanotechnologies of the late twentieth century. Thereby, it adds a novel historical chapter to the longstanding scientific and philosophical problem of the relationship between organisms and machines, now at the level of machine-like molecules. Investigating the history of research on proteins and cell membranes (an essential feature of life just as genes are), this book explores how life’s molecular machinery has been shaped by experimental investigation of active biological materials. It argues that the early 1970s saw a veritable “membrane moment,” in which fields such as bioenergetics, neurobiology, and synthetic biologies avant la lettre moved center stage, significantly reshaping the landscape of the molecular life sciences and highlighting the relevance of chemistry to this field’s recent development. Following the materialization of a “molecular pump” through research by key figures and institutions in America, the UK, and West Germany until c. 1990, this book draws a novel map of the molecular life sciences beyond genetics at the level of concepts, technique, and scope. By studying attempts to develop “biochips” in the 1980s, it also relates an early and surprising episode of bio- and nanotechnologies. Altogether, this book proposes novel historiographical and epistemological perspectives: to scrutinize changes to the materiality of life, to understand the relevance of chemistry for the late twentieth-century molecular life sciences, and to question their places and scientific persona.Less
This book tells the story of how a molecular-mechanical vision of life has become omnipresent in the sciences, biomedicine, and bio- and nanotechnologies of the late twentieth century. Thereby, it adds a novel historical chapter to the longstanding scientific and philosophical problem of the relationship between organisms and machines, now at the level of machine-like molecules. Investigating the history of research on proteins and cell membranes (an essential feature of life just as genes are), this book explores how life’s molecular machinery has been shaped by experimental investigation of active biological materials. It argues that the early 1970s saw a veritable “membrane moment,” in which fields such as bioenergetics, neurobiology, and synthetic biologies avant la lettre moved center stage, significantly reshaping the landscape of the molecular life sciences and highlighting the relevance of chemistry to this field’s recent development. Following the materialization of a “molecular pump” through research by key figures and institutions in America, the UK, and West Germany until c. 1990, this book draws a novel map of the molecular life sciences beyond genetics at the level of concepts, technique, and scope. By studying attempts to develop “biochips” in the 1980s, it also relates an early and surprising episode of bio- and nanotechnologies. Altogether, this book proposes novel historiographical and epistemological perspectives: to scrutinize changes to the materiality of life, to understand the relevance of chemistry for the late twentieth-century molecular life sciences, and to question their places and scientific persona.
Vivette Glover and Merton Sandler
- Published in print:
- 1990
- Published Online:
- March 2012
- ISBN:
- 9780192618108
- eISBN:
- 9780191724305
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780192618108.003.0019
- Subject:
- Neuroscience, Disorders of the Nervous System
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 ...
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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
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.
Noreen Tuross and Michael G. Campana
- Published in print:
- 2019
- Published Online:
- May 2020
- ISBN:
- 9780691195988
- eISBN:
- 9781400889730
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691195988.003.0007
- Subject:
- History, Ancient History / Archaeology
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 ...
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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
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.
Dennis Sherwood and Paul Dalby
- Published in print:
- 2018
- Published Online:
- August 2018
- ISBN:
- 9780198782957
- eISBN:
- 9780191826177
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198782957.001.0001
- Subject:
- Physics, Theoretical, Computational, and Statistical Physics
This book will equip a student of any physical or biological science with a sound understanding of thermodynamics, and will build confidence in using thermodynamics in practice. The emphasis is ...
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This book will equip a student of any physical or biological science with a sound understanding of thermodynamics, and will build confidence in using thermodynamics in practice. The emphasis is towards chemical thermodynamics, but the principles of the First, Second and Third Laws apply to all sciences. Importantly, the final four chapters show how thermodynamics can be applied to biological systems, discussing the biochemical standard state, bioenergetics, protein folding, and the self-assembly of smaller components to form higher-level structures. The book has not been written to support a particular curriculum; rather, it covers all the fundamental principles, so providing a comprehensive grounding, as well as a strong foundation for further study. It is therefore likely that there will be more material in this book than is required for any one particular curriculum, but we trust there is sufficient material for almost every curriculum. A key feature of the book is the style. It has been written so that ‘you can hear our voices’, and with the overarching intent of being logical, clear and comprehensible. The style will therefore be perceived as less formal than many other texts – and we trust more readable. Furthermore, we have sought to avoid phrases such as ‘it may be shown that...’, and ‘clearly, it follows that...’. If ‘it may be shown’, we show it; and we don’t use ‘clearly’ when things aren’t clear at all. Thermodynamics is notoriously difficult. This book does not make an intrinsically deep science ‘easy’. But it does make it intelligible.Less
This book will equip a student of any physical or biological science with a sound understanding of thermodynamics, and will build confidence in using thermodynamics in practice. The emphasis is towards chemical thermodynamics, but the principles of the First, Second and Third Laws apply to all sciences. Importantly, the final four chapters show how thermodynamics can be applied to biological systems, discussing the biochemical standard state, bioenergetics, protein folding, and the self-assembly of smaller components to form higher-level structures. The book has not been written to support a particular curriculum; rather, it covers all the fundamental principles, so providing a comprehensive grounding, as well as a strong foundation for further study. It is therefore likely that there will be more material in this book than is required for any one particular curriculum, but we trust there is sufficient material for almost every curriculum. A key feature of the book is the style. It has been written so that ‘you can hear our voices’, and with the overarching intent of being logical, clear and comprehensible. The style will therefore be perceived as less formal than many other texts – and we trust more readable. Furthermore, we have sought to avoid phrases such as ‘it may be shown that...’, and ‘clearly, it follows that...’. If ‘it may be shown’, we show it; and we don’t use ‘clearly’ when things aren’t clear at all. Thermodynamics is notoriously difficult. This book does not make an intrinsically deep science ‘easy’. But it does make it intelligible.
Betul Kacar
- Published in print:
- 2016
- Published Online:
- May 2017
- ISBN:
- 9780226401744
- eISBN:
- 9780226401911
- Item type:
- chapter
- Publisher:
- University of Chicago Press
- DOI:
- 10.7208/chicago/9780226401911.003.0012
- Subject:
- Philosophy, Philosophy of Science
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 ...
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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
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.
Zoltan Szallasi, Jorg Stelling, and Vipul Periwal (eds)
- Published in print:
- 2006
- Published Online:
- August 2013
- ISBN:
- 9780262195485
- eISBN:
- 9780262257060
- Item type:
- book
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262195485.001.0001
- Subject:
- Mathematics, Mathematical Biology
Research in systems biology requires the collaboration of researchers from diverse backgrounds, including biology, computer science, mathematics, statistics, physics, and biochemistry. These ...
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Research in systems biology requires the collaboration of researchers from diverse backgrounds, including biology, computer science, mathematics, statistics, physics, and biochemistry. These collaborations, necessary because of the enormous breadth of background needed for research in this field, can be hindered by differing understandings of the limitations and applicability of techniques and concerns from different disciplines. The emerging area of systems level modeling in cellular biology has lacked a critical and thorough overview. The book provides the necessary critical comparison of concepts and approaches, with an emphasis on their possible applications. It presents key concepts and their theoretical background, including the concepts of robustness and modularity and their exploitation to study biological systems; the best-known modeling approaches, and their advantages and disadvantages; lessons from the application of mathematical models to the study of cellular biology; and available modeling tools and datasets, along with their computational limitations.Less
Research in systems biology requires the collaboration of researchers from diverse backgrounds, including biology, computer science, mathematics, statistics, physics, and biochemistry. These collaborations, necessary because of the enormous breadth of background needed for research in this field, can be hindered by differing understandings of the limitations and applicability of techniques and concerns from different disciplines. The emerging area of systems level modeling in cellular biology has lacked a critical and thorough overview. The book provides the necessary critical comparison of concepts and approaches, with an emphasis on their possible applications. It presents key concepts and their theoretical background, including the concepts of robustness and modularity and their exploitation to study biological systems; the best-known modeling approaches, and their advantages and disadvantages; lessons from the application of mathematical models to the study of cellular biology; and available modeling tools and datasets, along with their computational limitations.
Angela N. H. Creager
- Published in print:
- 2013
- Published Online:
- January 2014
- ISBN:
- 9780226017808
- eISBN:
- 9780226017945
- Item type:
- book
- Publisher:
- University of Chicago Press
- DOI:
- 10.7208/chicago/9780226017945.001.0001
- Subject:
- History, History of Science, Technology, and Medicine
After World War II, the U.S. Atomic Energy Commission (AEC) began mass-producing radioisotopes in its Oak Ridge reactor, sending out nearly 64,000 shipments of radioactive materials to scientists and ...
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After World War II, the U.S. Atomic Energy Commission (AEC) began mass-producing radioisotopes in its Oak Ridge reactor, sending out nearly 64,000 shipments of radioactive materials to scientists and physicians by 1955. Even as the atomic bomb became the currency of the Cold War, radioisotopes represented the government’s efforts to harness power of the atom for peace—advancing medicine, domestic energy, and foreign relations. Radioisotopes provided physicians with new tools for diagnosis and therapy and equipped biologists to trace molecular transformations from metabolic pathways to ecosystems. However, the government’s attempt to present radioisotopes as marvelous dividends of the atomic age was undercut in the 1950s by the fallout debates, as scientists and citizens recognized the hazards of low-level radiation. The growing consciousness of the dangers of radioactivity did not reduce the demand for radioisotopes from hospitals and laboratories but did change their popular representation from being a therapeutic agent to an environmental poison. By the late twentieth century, public fears of radioactivity overshadowed any appreciation of the positive consequences of the AEC’s provision of radioisotopes for research and medicine. This book tells the story of how these radioisotopes, which were simultaneously scientific tools and political icons, transformed biomedicine and ecology.Less
After World War II, the U.S. Atomic Energy Commission (AEC) began mass-producing radioisotopes in its Oak Ridge reactor, sending out nearly 64,000 shipments of radioactive materials to scientists and physicians by 1955. Even as the atomic bomb became the currency of the Cold War, radioisotopes represented the government’s efforts to harness power of the atom for peace—advancing medicine, domestic energy, and foreign relations. Radioisotopes provided physicians with new tools for diagnosis and therapy and equipped biologists to trace molecular transformations from metabolic pathways to ecosystems. However, the government’s attempt to present radioisotopes as marvelous dividends of the atomic age was undercut in the 1950s by the fallout debates, as scientists and citizens recognized the hazards of low-level radiation. The growing consciousness of the dangers of radioactivity did not reduce the demand for radioisotopes from hospitals and laboratories but did change their popular representation from being a therapeutic agent to an environmental poison. By the late twentieth century, public fears of radioactivity overshadowed any appreciation of the positive consequences of the AEC’s provision of radioisotopes for research and medicine. This book tells the story of how these radioisotopes, which were simultaneously scientific tools and political icons, transformed biomedicine and ecology.
Mike Fortun
- Published in print:
- 2008
- Published Online:
- March 2012
- ISBN:
- 9780520247505
- eISBN:
- 9780520942615
- Item type:
- chapter
- Publisher:
- University of California Press
- DOI:
- 10.1525/california/9780520247505.003.0022
- Subject:
- Biology, Evolutionary Biology / Genetics
In 1999, deCODE Genetics printed a “code of ethics” written by “a group of deCODE employees,” with the Ethics Institute of the University of Iceland listed as “Advisors.” No people were listed, just ...
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In 1999, deCODE Genetics printed a “code of ethics” written by “a group of deCODE employees,” with the Ethics Institute of the University of Iceland listed as “Advisors.” No people were listed, just these collectivities. The twenty-page booklet with a heavy blue-paper cover was produced and mailed to the entire population of Iceland. As is often the case with ethics, and particularly codes of ethical principles, there is not a single concrete noun in deCODE's principles that signifies any specific historical, cultural, or institutional body or event; there is only a homogeneous population of bland abstractions. Biochemistry has more to do with ethics, in Halldór Laxness's view, than any theological or even humanist exegesis. “There is only one world in existence,” was the chord struck by the organist, “and in it there prevail either expedient or inexpedient conditions for those who are alive.” This elevation of “expediency” to a kind of ethical principle intrigued the author, and it kept reoccurring in Laxness's novel The Atom Station, often in tandem with biochemical references.Less
In 1999, deCODE Genetics printed a “code of ethics” written by “a group of deCODE employees,” with the Ethics Institute of the University of Iceland listed as “Advisors.” No people were listed, just these collectivities. The twenty-page booklet with a heavy blue-paper cover was produced and mailed to the entire population of Iceland. As is often the case with ethics, and particularly codes of ethical principles, there is not a single concrete noun in deCODE's principles that signifies any specific historical, cultural, or institutional body or event; there is only a homogeneous population of bland abstractions. Biochemistry has more to do with ethics, in Halldór Laxness's view, than any theological or even humanist exegesis. “There is only one world in existence,” was the chord struck by the organist, “and in it there prevail either expedient or inexpedient conditions for those who are alive.” This elevation of “expediency” to a kind of ethical principle intrigued the author, and it kept reoccurring in Laxness's novel The Atom Station, often in tandem with biochemical references.
Angela N. H. Creager
- Published in print:
- 2013
- Published Online:
- January 2014
- ISBN:
- 9780226017808
- eISBN:
- 9780226017945
- Item type:
- chapter
- Publisher:
- University of Chicago Press
- DOI:
- 10.7208/chicago/9780226017945.003.0007
- Subject:
- History, History of Science, Technology, and Medicine
This chapter follows radioisotopes into the laboratories of biochemists and molecular biologists, where they illuminated metabolic pathways and genetic transmission. Early isotope labelling ...
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This chapter follows radioisotopes into the laboratories of biochemists and molecular biologists, where they illuminated metabolic pathways and genetic transmission. Early isotope labelling experiments involved stable isotopes, but with the availability of radioisotopes from the AEC, biochemists began relying more on radioactive labels. The chapter features two case studies: Melvin Calvin and Andrew Benson’s elucidation of the steps of photosynthesis using carbon-14, and the role of sulfur-35 and phosphorus-32 in the 1953 Hershey-Chase experiment and other gene transfer experiments (including the so-called “suicide experiments” with phage). Both of these experiments helped establish radiolabeling as a central technique among biochemists and molecular biologists.Less
This chapter follows radioisotopes into the laboratories of biochemists and molecular biologists, where they illuminated metabolic pathways and genetic transmission. Early isotope labelling experiments involved stable isotopes, but with the availability of radioisotopes from the AEC, biochemists began relying more on radioactive labels. The chapter features two case studies: Melvin Calvin and Andrew Benson’s elucidation of the steps of photosynthesis using carbon-14, and the role of sulfur-35 and phosphorus-32 in the 1953 Hershey-Chase experiment and other gene transfer experiments (including the so-called “suicide experiments” with phage). Both of these experiments helped establish radiolabeling as a central technique among biochemists and molecular biologists.
Doogab Yi
- Published in print:
- 2015
- Published Online:
- September 2015
- ISBN:
- 9780226143835
- eISBN:
- 9780226216119
- Item type:
- chapter
- Publisher:
- University of Chicago Press
- DOI:
- 10.7208/chicago/9780226216119.003.0001
- Subject:
- History, History of Science, Technology, and Medicine
Chapter 1 examines the establishment of Stanford Medical School’s Biochemistry Department. I detail how this “DNA Department” developed its own style of research management and collaboration ...
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Chapter 1 examines the establishment of Stanford Medical School’s Biochemistry Department. I detail how this “DNA Department” developed its own style of research management and collaboration involving the financial and material arrangements among faculty members. Stanford biochemists’ moral and political economies of sharing provide an important background with which we can examine the dynamics between experimental developments and research environments.Less
Chapter 1 examines the establishment of Stanford Medical School’s Biochemistry Department. I detail how this “DNA Department” developed its own style of research management and collaboration involving the financial and material arrangements among faculty members. Stanford biochemists’ moral and political economies of sharing provide an important background with which we can examine the dynamics between experimental developments and research environments.
