Samir Okasha
- Published in print:
- 2006
- Published Online:
- January 2007
- ISBN:
- 9780199267972
- eISBN:
- 9780191708275
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199267972.001.0001
- Subject:
- Philosophy, Philosophy of Science
Does natural selection act primarily on individual organisms, on groups, on genes, or on whole species? This book provides a comprehensive analysis of the long-standing controversy in evolutionary ...
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Does natural selection act primarily on individual organisms, on groups, on genes, or on whole species? This book provides a comprehensive analysis of the long-standing controversy in evolutionary biology over the levels of selection, focusing on conceptual, philosophical, and foundational questions. In the first half of the book, a systematic framework is developed for thinking about natural selection acting at multiple levels of the biological hierarchy; the framework is then used to help resolve outstanding issues. Considerable attention is paid to the concept of causality as it relates to the levels of selection, particularly the idea that natural selection at one hierarchical level can have effects that ‘filter’ up or down to other levels. Full account is taken of the recent biological literature on ‘major evolutionary transitions’ and the recent resurgence of interest in multi-level selection theory among biologists. Other biological topics discussed include Price's equation, kin and group selection, the gene's eye view, evolutionary game theory, selfish genetic elements, species and clade selection, and the evolution of individuality. Philosophical topics discussed include reductionism and holism, causation and correlation, the nature of hierarchical organization, and realism and pluralism about the levels of selection.Less
Does natural selection act primarily on individual organisms, on groups, on genes, or on whole species? This book provides a comprehensive analysis of the long-standing controversy in evolutionary biology over the levels of selection, focusing on conceptual, philosophical, and foundational questions. In the first half of the book, a systematic framework is developed for thinking about natural selection acting at multiple levels of the biological hierarchy; the framework is then used to help resolve outstanding issues. Considerable attention is paid to the concept of causality as it relates to the levels of selection, particularly the idea that natural selection at one hierarchical level can have effects that ‘filter’ up or down to other levels. Full account is taken of the recent biological literature on ‘major evolutionary transitions’ and the recent resurgence of interest in multi-level selection theory among biologists. Other biological topics discussed include Price's equation, kin and group selection, the gene's eye view, evolutionary game theory, selfish genetic elements, species and clade selection, and the evolution of individuality. Philosophical topics discussed include reductionism and holism, causation and correlation, the nature of hierarchical organization, and realism and pluralism about the levels of selection.
Rosalind James and Theresa L. Pitts-Singer (eds)
- Published in print:
- 2008
- Published Online:
- September 2008
- ISBN:
- 9780195316957
- eISBN:
- 9780199871575
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195316957.001.0001
- Subject:
- Biology, Animal Biology, Plant Sciences and Forestry
Bees play a vital role as pollinators for many agricultural crops. This book discusses the interplay between bees, agriculture, and the environment. Although honey bees are well recognized as ...
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Bees play a vital role as pollinators for many agricultural crops. This book discusses the interplay between bees, agriculture, and the environment. Although honey bees are well recognized as pollinators, managed bumble bees and solitary bees are also critical for the successful pollination of certain crops, while wild bees provide a free service. As bees liberally pass pollen from one plant to the next, they also impact the broader ecosystem, and not always to the benefit of humankind. Bees can enhance the unintentional spread of genes from genetically engineered plants, and may increase the spread of invasive weeds. Conversely, genetically engineered plants can impact pollinators, and invasive weeds can supply new sources of food for these insects. Bees' flower-visiting activities also can be exploited to spread biological control agents that help to control crop pests. Bee pollination is important for production of native plants used for restoration of wild lands. Managing bees for pollination is complex and must consider bee natural history, physiology, pathology, and behavior. Furthermore, transporting bees from native ranges to new areas for pollination services can be controversial, and should be done only after assuring that a non-native bee introduction will not disrupt the ecosystem. Even though bees are small, unobtrusive creatures, they play large roles in the ecosystem. The connection between bees and humankind is symbolic of a broader interconnection between humans and the natural world.Less
Bees play a vital role as pollinators for many agricultural crops. This book discusses the interplay between bees, agriculture, and the environment. Although honey bees are well recognized as pollinators, managed bumble bees and solitary bees are also critical for the successful pollination of certain crops, while wild bees provide a free service. As bees liberally pass pollen from one plant to the next, they also impact the broader ecosystem, and not always to the benefit of humankind. Bees can enhance the unintentional spread of genes from genetically engineered plants, and may increase the spread of invasive weeds. Conversely, genetically engineered plants can impact pollinators, and invasive weeds can supply new sources of food for these insects. Bees' flower-visiting activities also can be exploited to spread biological control agents that help to control crop pests. Bee pollination is important for production of native plants used for restoration of wild lands. Managing bees for pollination is complex and must consider bee natural history, physiology, pathology, and behavior. Furthermore, transporting bees from native ranges to new areas for pollination services can be controversial, and should be done only after assuring that a non-native bee introduction will not disrupt the ecosystem. Even though bees are small, unobtrusive creatures, they play large roles in the ecosystem. The connection between bees and humankind is symbolic of a broader interconnection between humans and the natural world.
C. Neal Stewart
- Published in print:
- 2004
- Published Online:
- September 2007
- ISBN:
- 9780195157451
- eISBN:
- 9780199790388
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195157451.001.0001
- Subject:
- Biology, Biotechnology
From years prior to the release of the first commercial transgenic crop in 1995 to the present, many concerned activists, regulators, and scientists have questioned how genetic engineering might ...
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From years prior to the release of the first commercial transgenic crop in 1995 to the present, many concerned activists, regulators, and scientists have questioned how genetic engineering might impact the environment. No measurable negative environmental impacts have been observed for commercial genetically modified crops to date, even though several risks have been identified in experimental releases. Even so, none have approached doomsday scenarios posed by activists. The risks that have been extensively studied are gene flow from crops to weeds or crop landraces; side-effects of insecticidal transgenic proteins, such as accidental killing of monarch butterflies or beneficial insects; viral recombination; and transgene combinations. Close examination has uncovered no negative effects, but plenty of positive environmental impacts from growing crops engineered for insect resistance and herbicide resistance. Insect resistant cotton and corn kill only the insects that attempt to eat the crops and have saved several million gallons of chemical insecticide applications. Herbicide resistant soybean and corn have helped in soil conservation efforts since farmers do not have to use as much tillage to control weeds. In addition to these benefits, scientists are conducting research to produce genetically engineered plants to clean up toxins, produce plastics and biofuels, and perform other ecological services. The responsible use of genetic engineering is part of sustainable agriculture now and in the future.Less
From years prior to the release of the first commercial transgenic crop in 1995 to the present, many concerned activists, regulators, and scientists have questioned how genetic engineering might impact the environment. No measurable negative environmental impacts have been observed for commercial genetically modified crops to date, even though several risks have been identified in experimental releases. Even so, none have approached doomsday scenarios posed by activists. The risks that have been extensively studied are gene flow from crops to weeds or crop landraces; side-effects of insecticidal transgenic proteins, such as accidental killing of monarch butterflies or beneficial insects; viral recombination; and transgene combinations. Close examination has uncovered no negative effects, but plenty of positive environmental impacts from growing crops engineered for insect resistance and herbicide resistance. Insect resistant cotton and corn kill only the insects that attempt to eat the crops and have saved several million gallons of chemical insecticide applications. Herbicide resistant soybean and corn have helped in soil conservation efforts since farmers do not have to use as much tillage to control weeds. In addition to these benefits, scientists are conducting research to produce genetically engineered plants to clean up toxins, produce plastics and biofuels, and perform other ecological services. The responsible use of genetic engineering is part of sustainable agriculture now and in the future.
Jan Bures, F. Bermudez-Rattoni, and T. Yamamoto
- Published in print:
- 1998
- Published Online:
- January 2008
- ISBN:
- 9780198523475
- eISBN:
- 9780191712678
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198523475.001.0001
- Subject:
- Psychology, Neuropsychology
Conditioned taste aversion (CTA) is a robust defence device protecting animals against the repeated consumption of toxic food. CTA is due to an association of the gustatory conditional stimulus (CS) ...
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Conditioned taste aversion (CTA) is a robust defence device protecting animals against the repeated consumption of toxic food. CTA is due to an association of the gustatory conditional stimulus (CS) with the delayed visceral unconditional stimulus (US). Chapter 1 gives a brief survey of the history of CTA. Chapter 2 describes the methodology of behavioral tests undertaken. Chapter 3 reviews the centers in the brainstem, the diencephalon and insular cortex: the removal of which interferes with CTA. Chapter 4 deals with CTA disruption by local inactivation of insular cortex and of various extracortical regions. Chapter 5 describes drugs which can serve as US in CTA experiments or can block CTA retrieval. Chapter 6 describes the electrophysiology of neurons during formation or retrieval of CTA. Chapter 7 analyzes the interaction of gustatory and visceral afferents manifested by c-fos early genes. Chapter 8 concentrates on the possible repair of CTA blocking lesions by transplantation of fetal grafts. Chapter 9 discusses the paradoxes of CTA research, e.g., learning without awareness, CTA formed during blockade of proteosynthesis, or by rewarding drugs.Less
Conditioned taste aversion (CTA) is a robust defence device protecting animals against the repeated consumption of toxic food. CTA is due to an association of the gustatory conditional stimulus (CS) with the delayed visceral unconditional stimulus (US). Chapter 1 gives a brief survey of the history of CTA. Chapter 2 describes the methodology of behavioral tests undertaken. Chapter 3 reviews the centers in the brainstem, the diencephalon and insular cortex: the removal of which interferes with CTA. Chapter 4 deals with CTA disruption by local inactivation of insular cortex and of various extracortical regions. Chapter 5 describes drugs which can serve as US in CTA experiments or can block CTA retrieval. Chapter 6 describes the electrophysiology of neurons during formation or retrieval of CTA. Chapter 7 analyzes the interaction of gustatory and visceral afferents manifested by c-fos early genes. Chapter 8 concentrates on the possible repair of CTA blocking lesions by transplantation of fetal grafts. Chapter 9 discusses the paradoxes of CTA research, e.g., learning without awareness, CTA formed during blockade of proteosynthesis, or by rewarding drugs.
F.M.L. Thompson (ed.)
- Published in print:
- 2003
- Published Online:
- January 2013
- ISBN:
- 9780197262795
- eISBN:
- 9780191753954
- Item type:
- book
- Publisher:
- British Academy
- DOI:
- 10.5871/bacad/9780197262795.001.0001
- Subject:
- History, Cultural History
This book contains the texts of 17 lectures, delivered to the British Academy in 2001. Topics include Chinese Mountain Painting, prosperity and power in the age of Bede and Beowulf, Glyn Dwr, ...
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This book contains the texts of 17 lectures, delivered to the British Academy in 2001. Topics include Chinese Mountain Painting, prosperity and power in the age of Bede and Beowulf, Glyn Dwr, Shakespeare's sense of an exit, learning, liberty, poetry, social ethics, the House of Savoy during the Risorgimento, the disease of language and the language of disease, Gertrude Stein's differential syntax, Keith Douglas, Common Law's approach to property, Welfare-to-Work and genes.Less
This book contains the texts of 17 lectures, delivered to the British Academy in 2001. Topics include Chinese Mountain Painting, prosperity and power in the age of Bede and Beowulf, Glyn Dwr, Shakespeare's sense of an exit, learning, liberty, poetry, social ethics, the House of Savoy during the Risorgimento, the disease of language and the language of disease, Gertrude Stein's differential syntax, Keith Douglas, Common Law's approach to property, Welfare-to-Work and genes.
Quentin Cronk
- Published in print:
- 2009
- Published Online:
- May 2009
- ISBN:
- 9780199550357
- eISBN:
- 9780191720154
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199550357.001.1
- Subject:
- Biology, Plant Sciences and Forestry, Developmental Biology
This book surveys the momentous morphological change in plant evolution that created the terrestrial biosphere as we know it today. It takes as its premise that the study of plant evolution at its ...
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This book surveys the momentous morphological change in plant evolution that created the terrestrial biosphere as we know it today. It takes as its premise that the study of plant evolution at its grandest is the study of how mutations in genes have changed the way the planet functions. The evolution of the leaf, for instance, change terrestrial carbon cycling and primary productivity, so changing the earth's atmosphere and the distribution of carbon. The book charts the rise to complexity of the three many organs systems of complex land plants, the axis or stem, the leaf, and the root. These organs system are surveyed morphologically in the light of empirical morphology, in which organ concepts are considered as hypotheses to be tested in a developmental, molecular, and phylogenetic framework. It also tackles the evolution of the seed (via heterospory and covering of the megasporangium) and the flower (by complex patterning of sporophylls and sterile phyllomes). All this is placed where possible in its molecular context, with the aim of demonstrating how evolving gene networks have given rise to increasing morphological complexity.Less
This book surveys the momentous morphological change in plant evolution that created the terrestrial biosphere as we know it today. It takes as its premise that the study of plant evolution at its grandest is the study of how mutations in genes have changed the way the planet functions. The evolution of the leaf, for instance, change terrestrial carbon cycling and primary productivity, so changing the earth's atmosphere and the distribution of carbon. The book charts the rise to complexity of the three many organs systems of complex land plants, the axis or stem, the leaf, and the root. These organs system are surveyed morphologically in the light of empirical morphology, in which organ concepts are considered as hypotheses to be tested in a developmental, molecular, and phylogenetic framework. It also tackles the evolution of the seed (via heterospory and covering of the megasporangium) and the flower (by complex patterning of sporophylls and sterile phyllomes). All this is placed where possible in its molecular context, with the aim of demonstrating how evolving gene networks have given rise to increasing morphological complexity.
Carsten Wiuf and Claus L. Andersen (eds)
- Published in print:
- 2009
- Published Online:
- September 2009
- ISBN:
- 9780199532872
- eISBN:
- 9780191714467
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199532872.001.0001
- Subject:
- Mathematics, Probability / Statistics, Biostatistics
This book discusses novel advances in informatics and statistics in molecular cancer research. Through eight chapters it discusses specific topics in cancer research, talks about how the topics give ...
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This book discusses novel advances in informatics and statistics in molecular cancer research. Through eight chapters it discusses specific topics in cancer research, talks about how the topics give rise to development of new informatics and statistics tools, and explains how the tools can be applied. The focus of the book is to provide an understanding of key concepts and tools, rather than focusing on technical issues. A main theme is the extensive use of array technologies in modern cancer research — gene expression and exon arrays, SNP and copy number arrays and methylation arrays — to derive quantitative and qualitative statements about cancer, its progression and aetiology, and to understand how these technologies at one hand allow us learn about cancer tissue as a complex system and at the other hand allow us to pinpoint key genes and events as crucial for the development of the disease. Cancer is characterized by genetic and genomic alterations that influence all levels of the cell's machinery and function.Less
This book discusses novel advances in informatics and statistics in molecular cancer research. Through eight chapters it discusses specific topics in cancer research, talks about how the topics give rise to development of new informatics and statistics tools, and explains how the tools can be applied. The focus of the book is to provide an understanding of key concepts and tools, rather than focusing on technical issues. A main theme is the extensive use of array technologies in modern cancer research — gene expression and exon arrays, SNP and copy number arrays and methylation arrays — to derive quantitative and qualitative statements about cancer, its progression and aetiology, and to understand how these technologies at one hand allow us learn about cancer tissue as a complex system and at the other hand allow us to pinpoint key genes and events as crucial for the development of the disease. Cancer is characterized by genetic and genomic alterations that influence all levels of the cell's machinery and function.
Minoru Fukuda, Urs Rutishauser, and Ronald L. Schnaar (eds)
- Published in print:
- 2005
- Published Online:
- September 2009
- ISBN:
- 9780198525387
- eISBN:
- 9780191723872
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198525387.001.0001
- Subject:
- Neuroscience, Molecular and Cellular Systems
In the past decade, there have been tremendous developments in the understanding of the structure, biosynthesis, and function of glycoconjugates present in the nervous system. These developments were ...
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In the past decade, there have been tremendous developments in the understanding of the structure, biosynthesis, and function of glycoconjugates present in the nervous system. These developments were initiated by advances in the molecular cloning of glycosyltransferases that direct the synthesis of these complex carbohydrates. In particular, the molecular cloning of polysialyltransferases, HNK-1 sulfotransferase, ganglioside sialyltransferases, and proteoglycan sulfotransferases provided a great opportunity to determine the roles of these glycans in the nervous system. Moreover, the availability of gene inactivation by homologous recombination in mouse, the ‘knockout mouse’, has led to an explosion of knowledge in understanding the physiological functions of glycoconjugates during embryonic development and organogenesis. In certain studies, the physiological function of glycoconjugates in adult mice can be evaluated in depth by examining the phenotype of adult knockout mice. This book focuses on topics in and expands descriptions of neuroglycobiology, based on recent advances in this field. The book includes eight chapters from various authors representing the field of neuroglycobiology. In the first two chapters, the biosynthesis and roles of glycoprotein glycosylation are described. Chapter 3 describes HNK-1 glycans. Chapter 4 describes the biosynthesis and roles of the brain glycolipids. The biosynthetic pathway and the roles of gangliosides based on gene knockout mice are described in Chapter 5. The final two chapters are devoted to summarizing recent findings on diseases caused by abnormal metabolism in glycoproteins and glycolipids.Less
In the past decade, there have been tremendous developments in the understanding of the structure, biosynthesis, and function of glycoconjugates present in the nervous system. These developments were initiated by advances in the molecular cloning of glycosyltransferases that direct the synthesis of these complex carbohydrates. In particular, the molecular cloning of polysialyltransferases, HNK-1 sulfotransferase, ganglioside sialyltransferases, and proteoglycan sulfotransferases provided a great opportunity to determine the roles of these glycans in the nervous system. Moreover, the availability of gene inactivation by homologous recombination in mouse, the ‘knockout mouse’, has led to an explosion of knowledge in understanding the physiological functions of glycoconjugates during embryonic development and organogenesis. In certain studies, the physiological function of glycoconjugates in adult mice can be evaluated in depth by examining the phenotype of adult knockout mice. This book focuses on topics in and expands descriptions of neuroglycobiology, based on recent advances in this field. The book includes eight chapters from various authors representing the field of neuroglycobiology. In the first two chapters, the biosynthesis and roles of glycoprotein glycosylation are described. Chapter 3 describes HNK-1 glycans. Chapter 4 describes the biosynthesis and roles of the brain glycolipids. The biosynthetic pathway and the roles of gangliosides based on gene knockout mice are described in Chapter 5. The final two chapters are devoted to summarizing recent findings on diseases caused by abnormal metabolism in glycoproteins and glycolipids.
Baltazar Aguda, Avner Friedman, and Visiting Associate Professor, The Ohio State University
- Published in print:
- 2008
- Published Online:
- September 2008
- ISBN:
- 9780198570912
- eISBN:
- 9780191718717
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198570912.001.0001
- Subject:
- Physics, Soft Matter / Biological Physics
The human genome of three billion letters has been sequenced. So have the genomes of thousands of other organisms. With unprecedented resolution, modern technologies are allowing us to peek into the ...
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The human genome of three billion letters has been sequenced. So have the genomes of thousands of other organisms. With unprecedented resolution, modern technologies are allowing us to peek into the world of genes, biomolecules, and cells, and flooding us with data of immense complexity that we are just barely beginning to understand. A huge gap separates our knowledge of the components of a cell and what is known from our observations of its physiology. This book explores what has been done to close this gap of understanding between the realms of molecules and biological processes. It contains illustrative mechanisms and models of gene regulatory networks, DNA replication, the cell cycle, cell death, differentiation, cell senescence, and the abnormal state of cancer cells. The mechanisms are biomolecular in detail, and the models are mathematical in nature.Less
The human genome of three billion letters has been sequenced. So have the genomes of thousands of other organisms. With unprecedented resolution, modern technologies are allowing us to peek into the world of genes, biomolecules, and cells, and flooding us with data of immense complexity that we are just barely beginning to understand. A huge gap separates our knowledge of the components of a cell and what is known from our observations of its physiology. This book explores what has been done to close this gap of understanding between the realms of molecules and biological processes. It contains illustrative mechanisms and models of gene regulatory networks, DNA replication, the cell cycle, cell death, differentiation, cell senescence, and the abnormal state of cancer cells. The mechanisms are biomolecular in detail, and the models are mathematical in nature.
Paul F. Lurquin and Linda Stone
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780195315387
- eISBN:
- 9780199785674
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195315387.003.0006
- Subject:
- Religion, Religion and Society
First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas ...
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First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas in the atmosphere. Later, eukaryotes appeared and diversified through mutation and gene duplication (including mutation and duplication of master genes), which led to the rewiring of entire gene networks. The chapter shows that there is no fundamental difference between macroevolution and microevolution. It shows that making artificial life in the lab as well as transgenic life-forms would be impossible if the Intelligent Design scenario were correct. Indeed, ID posits that living systems were holistically designed and thus cannot be constructed in a piecemeal fashion.Less
First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas in the atmosphere. Later, eukaryotes appeared and diversified through mutation and gene duplication (including mutation and duplication of master genes), which led to the rewiring of entire gene networks. The chapter shows that there is no fundamental difference between macroevolution and microevolution. It shows that making artificial life in the lab as well as transgenic life-forms would be impossible if the Intelligent Design scenario were correct. Indeed, ID posits that living systems were holistically designed and thus cannot be constructed in a piecemeal fashion.
Samir Okasha
- Published in print:
- 2006
- Published Online:
- January 2007
- ISBN:
- 9780199267972
- eISBN:
- 9780191708275
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199267972.003.0005
- Subject:
- Philosophy, Philosophy of Science
This chapter examines the ‘genic’ view of evolution associated with Williams, Dawkins, Maynard Smith, and others. A distinction is drawn between the process of genic selection and a gene's eye ...
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This chapter examines the ‘genic’ view of evolution associated with Williams, Dawkins, Maynard Smith, and others. A distinction is drawn between the process of genic selection and a gene's eye perspective on selection processes that occur at other levels. Outlaw genes or selfish genetic elements, which spread at the expense of other genes in the same organism, are briefly examined and the use of multi-level selection theory to explore the evolutionary dynamics of outlaws is discussed. A number of objections to gene's eye thinking are examined, including the charge of ‘confusing bookkeeping with causality’ and the charge of ignoring the context-dependence of genes' effects on phenotype.Less
This chapter examines the ‘genic’ view of evolution associated with Williams, Dawkins, Maynard Smith, and others. A distinction is drawn between the process of genic selection and a gene's eye perspective on selection processes that occur at other levels. Outlaw genes or selfish genetic elements, which spread at the expense of other genes in the same organism, are briefly examined and the use of multi-level selection theory to explore the evolutionary dynamics of outlaws is discussed. A number of objections to gene's eye thinking are examined, including the charge of ‘confusing bookkeeping with causality’ and the charge of ignoring the context-dependence of genes' effects on phenotype.
Alessandro Minelli
- Published in print:
- 2008
- Published Online:
- May 2009
- ISBN:
- 9780198566205
- eISBN:
- 9780191713866
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198566205.003.0002
- Subject:
- Biology, Animal Biology, Evolutionary Biology / Genetics
The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially ...
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The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially increasing amount of molecular sequence data, to be analysed through increasingly sophisticated algorithms. Progress has been overcoming the pitfalls of earlier naïve hypotheses, such as the putatively uniform rate of the molecular clock across lineages, as well as problems deriving from gene duplication, gene loss, and horizontal gene transfer. However, the intrinsic limits of the resolution power of sequence comparisons are also emerging, as in the case of geologically old sequences of a series of branchings of the phylogenetic tree, which reduce in practice to multibranched star-shaped phylogenies. The single best source of data for the molecular phylogeny of the Metazoa is arguably the mitochondrial genome, in terms of gene, genome sequences, and also gene orderLess
The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially increasing amount of molecular sequence data, to be analysed through increasingly sophisticated algorithms. Progress has been overcoming the pitfalls of earlier naïve hypotheses, such as the putatively uniform rate of the molecular clock across lineages, as well as problems deriving from gene duplication, gene loss, and horizontal gene transfer. However, the intrinsic limits of the resolution power of sequence comparisons are also emerging, as in the case of geologically old sequences of a series of branchings of the phylogenetic tree, which reduce in practice to multibranched star-shaped phylogenies. The single best source of data for the molecular phylogeny of the Metazoa is arguably the mitochondrial genome, in terms of gene, genome sequences, and also gene order
Günter P. Wagner
- Published in print:
- 2014
- Published Online:
- October 2017
- ISBN:
- 9780691156460
- eISBN:
- 9781400851461
- Item type:
- book
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691156460.001.0001
- Subject:
- Biology, Evolutionary Biology / Genetics
Homology—a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird's wing—is one of the most fundamental yet challenging concepts in evolutionary ...
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Homology—a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird's wing—is one of the most fundamental yet challenging concepts in evolutionary biology. This book provides the first mechanistically based theory of what homology is and how it arises in evolution. The book argues that homology, or character identity, can be explained through the historical continuity of character identity networks—that is, the gene regulatory networks that enable differential gene expression. It shows how character identity is independent of the form and function of the character itself because the same network can activate different effector genes and thus control the development of different shapes, sizes, and qualities of the character. Demonstrating how this theoretical model can provide a foundation for understanding the evolutionary origin of novel characters, the book applies it to the origin and evolution of specific systems, such as cell types; skin, hair, and feathers; limbs and digits; and flowers. The first major synthesis of homology to be published in decades, this book reveals how a mechanistically based theory can serve as a unifying concept for any branch of science concerned with the structure and development of organisms, and how it can help explain major transitions in evolution and broad patterns of biological diversity.Less
Homology—a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird's wing—is one of the most fundamental yet challenging concepts in evolutionary biology. This book provides the first mechanistically based theory of what homology is and how it arises in evolution. The book argues that homology, or character identity, can be explained through the historical continuity of character identity networks—that is, the gene regulatory networks that enable differential gene expression. It shows how character identity is independent of the form and function of the character itself because the same network can activate different effector genes and thus control the development of different shapes, sizes, and qualities of the character. Demonstrating how this theoretical model can provide a foundation for understanding the evolutionary origin of novel characters, the book applies it to the origin and evolution of specific systems, such as cell types; skin, hair, and feathers; limbs and digits; and flowers. The first major synthesis of homology to be published in decades, this book reveals how a mechanistically based theory can serve as a unifying concept for any branch of science concerned with the structure and development of organisms, and how it can help explain major transitions in evolution and broad patterns of biological diversity.
Paul F. Lurquin and Linda Stone
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780195315387
- eISBN:
- 9780199785674
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195315387.003.0003
- Subject:
- Religion, Religion and Society
This chapter rebuts irreducible complexity and creationism by explaining the reliability of dating techniques as well as sophisticated laboratory techniques that allow researchers to synthesize ...
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This chapter rebuts irreducible complexity and creationism by explaining the reliability of dating techniques as well as sophisticated laboratory techniques that allow researchers to synthesize extinct genes (genetic archaeology, gene resurrection) and study their homology to other genes. These techniques clearly demonstrate that the irreducible complexity of the eye, the immune system, and the bacterial flagellum are subjective impressions. On the contrary, phylogenetic trees based on gene homology show a deep evolutionary link between simple life-forms and complex ones. Finally, the chapter gives several examples of “poor design” that cast doubt on the principle of Intelligent Design.Less
This chapter rebuts irreducible complexity and creationism by explaining the reliability of dating techniques as well as sophisticated laboratory techniques that allow researchers to synthesize extinct genes (genetic archaeology, gene resurrection) and study their homology to other genes. These techniques clearly demonstrate that the irreducible complexity of the eye, the immune system, and the bacterial flagellum are subjective impressions. On the contrary, phylogenetic trees based on gene homology show a deep evolutionary link between simple life-forms and complex ones. Finally, the chapter gives several examples of “poor design” that cast doubt on the principle of Intelligent Design.
Nikolas Rose and Joelle M. Abi-Rached
- Published in print:
- 2013
- Published Online:
- October 2017
- ISBN:
- 9780691149608
- eISBN:
- 9781400846337
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691149608.003.0002
- Subject:
- Neuroscience, Development
This chapter examines the neuromolecular and plastic brain. Ideas about plasticity and the openness of brains to environment influences, from initial evidence about nerve development, through the ...
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This chapter examines the neuromolecular and plastic brain. Ideas about plasticity and the openness of brains to environment influences, from initial evidence about nerve development, through the recognition that synaptic plasticity was the very basis of learning and memory, to evidence about the influence of environment on gene expression and the persistence throughout life of the capacity to make new neurons—all this made the neuromolecular brain seem exquisitely open to its milieu, with changes at the molecular level occurring throughout the course of a human life and thus shaping the growth, organization, and regeneration of neurons and neuronal circuits at time scales from the millisecond to the decade. This was an opportunity to explore the myriad ways in which the milieu got “under the skin,” implying an openness of these molecular processes of the brain to biography, sociality, and culture, and hence perhaps even to history and politics.Less
This chapter examines the neuromolecular and plastic brain. Ideas about plasticity and the openness of brains to environment influences, from initial evidence about nerve development, through the recognition that synaptic plasticity was the very basis of learning and memory, to evidence about the influence of environment on gene expression and the persistence throughout life of the capacity to make new neurons—all this made the neuromolecular brain seem exquisitely open to its milieu, with changes at the molecular level occurring throughout the course of a human life and thus shaping the growth, organization, and regeneration of neurons and neuronal circuits at time scales from the millisecond to the decade. This was an opportunity to explore the myriad ways in which the milieu got “under the skin,” implying an openness of these molecular processes of the brain to biography, sociality, and culture, and hence perhaps even to history and politics.
Igor B. Rogozin, Yuri I. Wolf, Vladimir N. Babenko, and Eugene V. Koonin
- Published in print:
- 2006
- Published Online:
- September 2007
- ISBN:
- 9780199297306
- eISBN:
- 9780191713729
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199297306.003.0011
- Subject:
- Biology, Evolutionary Biology / Genetics
The Dollo parsimony method is based on the assumption that a complex character that has been lost during evolution of a particular lineage cannot be regained. When applicable, this principle leads to ...
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The Dollo parsimony method is based on the assumption that a complex character that has been lost during evolution of a particular lineage cannot be regained. When applicable, this principle leads to a substantial simplification of evolutionary analysis and provides for unambiguous reconstruction of evolutionary scenarios, which may not be attainable with other methods. In this chapter, applications of Dollo parsimony are described for the quantitative analysis of the dynamics of genome evolution. Dollo parsimony is the method of choice for reconstructing evolution of the gene repertoire of eukaryotic organisms because although multiple, independent losses of a gene in different lineages are common, multiple gains of the same gene are improbable. This contrasts with the situation in prokaryotes where the widespread occurrence of horizontal gene transfer makes multiple gains possible, thereby invalidating the Dollo principle. The chapter applies Dollo parsimony to reconstruct the scenario of evolution for the genomes of crown-group eukaryotes by assigning the loss of genes and emergence of new genes to the branches of the phylogenetic tree, and delineate the minimal gene sets for various ancestral forms. A similar analysis, with rather unexpected results, was performed to infer gain versus loss of introns in conserved eukaryotic genes. The applicability of the Dollo principle for these and other problems in evolutionary genomics is discussed.Less
The Dollo parsimony method is based on the assumption that a complex character that has been lost during evolution of a particular lineage cannot be regained. When applicable, this principle leads to a substantial simplification of evolutionary analysis and provides for unambiguous reconstruction of evolutionary scenarios, which may not be attainable with other methods. In this chapter, applications of Dollo parsimony are described for the quantitative analysis of the dynamics of genome evolution. Dollo parsimony is the method of choice for reconstructing evolution of the gene repertoire of eukaryotic organisms because although multiple, independent losses of a gene in different lineages are common, multiple gains of the same gene are improbable. This contrasts with the situation in prokaryotes where the widespread occurrence of horizontal gene transfer makes multiple gains possible, thereby invalidating the Dollo principle. The chapter applies Dollo parsimony to reconstruct the scenario of evolution for the genomes of crown-group eukaryotes by assigning the loss of genes and emergence of new genes to the branches of the phylogenetic tree, and delineate the minimal gene sets for various ancestral forms. A similar analysis, with rather unexpected results, was performed to infer gain versus loss of introns in conserved eukaryotic genes. The applicability of the Dollo principle for these and other problems in evolutionary genomics is discussed.
Michael L. Arnold
- Published in print:
- 2007
- Published Online:
- April 2010
- ISBN:
- 9780199229031
- eISBN:
- 9780191728266
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199229031.003.0010
- Subject:
- Biology, Evolutionary Biology / Genetics
This chapter begins by reflecting upon the major theme of this book: that genetic exchange is pervasive across all biological lineages. It discusses the implications of this regarding the ...
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This chapter begins by reflecting upon the major theme of this book: that genetic exchange is pervasive across all biological lineages. It discusses the implications of this regarding the tree-of-life and web-of-life concepts. Research directions that will benefit our understanding of the role of genetic exchange in evolution are also discussed. Some of these, including the use of genomic information to discern web processes, are gaining momentum with the appearance of many new data-sets. Others, such as studies that investigate the role of ecological setting on the outcome of genetic exchange, are rare, yet they represent another Golden Fleece because of their potential to yield new insights of major importance.Less
This chapter begins by reflecting upon the major theme of this book: that genetic exchange is pervasive across all biological lineages. It discusses the implications of this regarding the tree-of-life and web-of-life concepts. Research directions that will benefit our understanding of the role of genetic exchange in evolution are also discussed. Some of these, including the use of genomic information to discern web processes, are gaining momentum with the appearance of many new data-sets. Others, such as studies that investigate the role of ecological setting on the outcome of genetic exchange, are rare, yet they represent another Golden Fleece because of their potential to yield new insights of major importance.
Beverley J. Glover
- Published in print:
- 2007
- Published Online:
- January 2008
- ISBN:
- 9780198565970
- eISBN:
- 9780191714009
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198565970.003.0009
- Subject:
- Biology, Plant Sciences and Forestry
It is becoming clear that flower development is a cascade, with flowering time integrators activating floral meristem identity genes which activate floral organ identity genes. The floral organ ...
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It is becoming clear that flower development is a cascade, with flowering time integrators activating floral meristem identity genes which activate floral organ identity genes. The floral organ identity genes themselves encode transcription factors, and are predicted to activate the many structural genes required to form the new organs, as well as further regulatory genes controlling processes such as pigment synthesis. The expression patterns of the floral organ identity genes determine the positions of developing organs (in the ABC model of flower development), and those expression patterns are themselves determined in part by cadastral genes (genes whose function is to specify the domain of expression of other genes). Floral organ identity genes act together as transcriptional complexes to ensure expression of the correct structural genes in each whorl of the developing flower.Less
It is becoming clear that flower development is a cascade, with flowering time integrators activating floral meristem identity genes which activate floral organ identity genes. The floral organ identity genes themselves encode transcription factors, and are predicted to activate the many structural genes required to form the new organs, as well as further regulatory genes controlling processes such as pigment synthesis. The expression patterns of the floral organ identity genes determine the positions of developing organs (in the ABC model of flower development), and those expression patterns are themselves determined in part by cadastral genes (genes whose function is to specify the domain of expression of other genes). Floral organ identity genes act together as transcriptional complexes to ensure expression of the correct structural genes in each whorl of the developing flower.
Anthony O'Hear
- Published in print:
- 1999
- Published Online:
- November 2003
- ISBN:
- 9780198250043
- eISBN:
- 9780191598111
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/0198250045.001.0001
- Subject:
- Philosophy, Philosophy of Science
The theory of evolution may be successful in explaining natural history, but it is of limited value when applied to the human world. Because of our reflectiveness and rationality, as embodied in ...
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The theory of evolution may be successful in explaining natural history, but it is of limited value when applied to the human world. Because of our reflectiveness and rationality, as embodied in language, we give ourselves ideals that cannot be justified in terms of survival‐promotion or reproductive advantage. Evolutionary theory is unable to give satisfactory accounts of such distinctive features of human life as the quest for knowledge, our moral sense, and the appreciation of beauty. At most, it can account for their prefiguration at some earlier stage of development than the human. In all these areas we transcend our biological origins, and such mechanisms as genetic survival, kin selection, reciprocal altruism, and sexual selection. But because of our rationality we can also transcend our cultural inheritance explanation of which in terms of memes is both hollow and misleading. We are rooted both in our biology and in our cultural inheritance; but, sociobiology and sociology notwithstanding, we are prisoners neither of our genes nor of the ideas we encounter as we each make our personal journey through life.Less
The theory of evolution may be successful in explaining natural history, but it is of limited value when applied to the human world. Because of our reflectiveness and rationality, as embodied in language, we give ourselves ideals that cannot be justified in terms of survival‐promotion or reproductive advantage. Evolutionary theory is unable to give satisfactory accounts of such distinctive features of human life as the quest for knowledge, our moral sense, and the appreciation of beauty. At most, it can account for their prefiguration at some earlier stage of development than the human. In all these areas we transcend our biological origins, and such mechanisms as genetic survival, kin selection, reciprocal altruism, and sexual selection. But because of our rationality we can also transcend our cultural inheritance explanation of which in terms of memes is both hollow and misleading. We are rooted both in our biology and in our cultural inheritance; but, sociobiology and sociology notwithstanding, we are prisoners neither of our genes nor of the ideas we encounter as we each make our personal journey through life.
Peter Kraft and David J. Hunter
- Published in print:
- 2009
- Published Online:
- May 2010
- ISBN:
- 9780195398441
- eISBN:
- 9780199776023
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195398441.003.0009
- Subject:
- Public Health and Epidemiology, Public Health, Epidemiology
This chapter discusses the study of gene-environment and gene-gene interactions in genetic epidemiology. It starts with a review of the definition of statistical gene-environment interaction, which ...
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This chapter discusses the study of gene-environment and gene-gene interactions in genetic epidemiology. It starts with a review of the definition of statistical gene-environment interaction, which is what is typically measured and reported in genetic association studies, and contrasts this with specific theoretical and general intuitive models for biologic interaction. It then describes how these concepts can be extended to the study of gene-gene interactions, and reviews available study designs, with particular emphasis on estimating joint gene-environment and gene-gene effects.Less
This chapter discusses the study of gene-environment and gene-gene interactions in genetic epidemiology. It starts with a review of the definition of statistical gene-environment interaction, which is what is typically measured and reported in genetic association studies, and contrasts this with specific theoretical and general intuitive models for biologic interaction. It then describes how these concepts can be extended to the study of gene-gene interactions, and reviews available study designs, with particular emphasis on estimating joint gene-environment and gene-gene effects.
