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Introductory Concepts

Domitilla Del Vecchio and Richard M. Murray

in Biomolecular Feedback Systems

Published in print:
2014
Published Online:
October 2017
ISBN:
9780691161532
eISBN:
9781400850501
Item type:
chapter
Publisher:
Princeton University Press
DOI:
10.23943/princeton/9780691161532.003.0001
Subject:
Biology, Biochemistry / Molecular Biology

This chapter provides a brief introduction to concepts from systems biology; tools from differential equations and control theory; and approaches to the modeling, analysis, and design of biomolecular ... More


General Features of Life

Gennaro Auletta

in Cognitive Biology: Dealing with Information from Bacteria to Minds

Published in print:
2011
Published Online:
September 2011
ISBN:
9780199608485
eISBN:
9780191729539
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199608485.003.0008
Subject:
Physics, Soft Matter / Biological Physics

Here, the proper notion of a biological system is introduced. This notion implies the combination of a metabolism, of a genetic system, and of a selective system.


Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False

Thomas Nagel

Published in print:
2012
Published Online:
January 2013
ISBN:
9780199919758
eISBN:
9780199980369
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199919758.001.0001
Subject:
Philosophy, General, Philosophy of Science

This book argues that the widely accepted world view of materialist naturalism is untenable. The mind-body problem cannot be confined to the relation between animal minds and animal bodies. If ... More


From Bacteria to Belief: Immunity and Security

Luis P. Villarreal

in Natural Security: A Darwinian Approach to a Dangerous World

Published in print:
2008
Published Online:
March 2012
ISBN:
9780520253476
eISBN:
9780520934313
Item type:
chapter
Publisher:
University of California Press
DOI:
10.1525/california/9780520253476.003.0004
Subject:
Biology, Evolutionary Biology / Genetics

Biological systems must employ a security or immunity system to ensure their survival. This chapter traces the early origins of biological identification and immune systems, first found in the ... More


The Work of Biological Individuality: Concepts and Contexts

Scott Lidgard and Lynn K. Nyhart

in Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives

Published in print:
2017
Published Online:
January 2018
ISBN:
9780226446318
eISBN:
9780226446592
Item type:
chapter
Publisher:
University of Chicago Press
DOI:
10.7208/chicago/9780226446592.003.0002
Subject:
History, History of Science, Technology, and Medicine

Why are there so many concepts of biological individuality? This chapter shows that a wide range of definitional criteria of individuality has been integral to biological studies for at least 170 ... More


Model Systems, Model Organisms

Rowland H. Davis

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

Published in print:
2003
Published Online:
April 2010
ISBN:
9780195154368
eISBN:
9780199893935
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780195154368.003.0001
Subject:
Biology, Biochemistry / Molecular Biology

Natural philosophers and biologists of the past sought to make sense of the many types of plants and creatures that, if not made for humans, were at least created by imaginative gods. As the ... More


Complexity and Robustness of Cellular Systems

Jörg Stelling, Uwe Sauer, Francis J. Doyle, and John Doyle

in System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Published in print:
2006
Published Online:
August 2013
ISBN:
9780262195485
eISBN:
9780262257060
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262195485.003.0002
Subject:
Mathematics, Mathematical Biology

This chapter focuses on the connections between cellular complexity and robustness—with robustness requirements being the driving forces for complexity. It begins by describing the sources and types ... More


Plasticity and Complexity in Biology: Topological Organization, Regulatory Protein Networks, and Mechanisms of Genetic Expression

Luciano Boi

in Information and Living Systems: Philosophical and Scientific Perspectives

Published in print:
2011
Published Online:
August 2013
ISBN:
9780262201742
eISBN:
9780262295246
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262201742.003.0009
Subject:
Philosophy, Philosophy of Science

This chapter studies a number of important aspects related to the plasticity and complexity of biological systems and their links. The relationship between the topological organization and dynamics ... More


The Microbial Models of Molecular Biology: From Genes to Genomes

Rowland H. Davis

Published in print:
2003
Published Online:
April 2010
ISBN:
9780195154368
eISBN:
9780199893935
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780195154368.001.0001
Subject:
Biology, Biochemistry / Molecular Biology

This book explains the role of simple biological model systems in the growth of molecular biology. Essentially, the whole history of molecular biology is presented here, tracing the work in ... More


The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems

Andreas Wagner

Published in print:
2011
Published Online:
December 2013
ISBN:
9780199692590
eISBN:
9780191774829
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199692590.001.0001
Subject:
Biology, Evolutionary Biology / Genetics

The history of life is a nearly four billion-year-old story of transformative change. This change ranges from dramatic macroscopic innovations such as the evolution of wings or eyes, to a myriad of ... More


On Modules and Modularity

Zoltan Szallasi, Vipul Periwal, and Jörg Stelling

in System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Published in print:
2006
Published Online:
August 2013
ISBN:
9780262195485
eISBN:
9780262257060
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262195485.003.0003
Subject:
Mathematics, Mathematical Biology

The complexity of biological systems requires unifying, simplifying concepts that might allow a predictive understanding of their functioning. Suggestions for such concepts include “modularity” along ... More


The Role of Modeling in Systems Biology

Douglas B. Kell and Joshua D. Knowles

in System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Published in print:
2006
Published Online:
August 2013
ISBN:
9780262195485
eISBN:
9780262257060
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262195485.003.0001
Subject:
Mathematics, Mathematical Biology

This chapter discusses some of the reasons for seeking to model complex cellular biological systems. It begins by presenting a philosophical overview and historical context. It then considers the ... More


Bodily Parts in the Structure-Function Dialectic

Ingo Brigandt

in Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives

Published in print:
2017
Published Online:
January 2018
ISBN:
9780226446318
eISBN:
9780226446592
Item type:
chapter
Publisher:
University of Chicago Press
DOI:
10.7208/chicago/9780226446592.003.0011
Subject:
History, History of Science, Technology, and Medicine

Understanding the organization of an organism by individuating meaningful parts and accounting for organismal properties by studying the interaction of bodily parts is a central practice in many ... More


Qualitative Approaches to the Analysis of Genetic Regulatory Networks

Hidde de Jong and Delphine Ropers

in System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Published in print:
2006
Published Online:
August 2013
ISBN:
9780262195485
eISBN:
9780262257060
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262195485.003.0007
Subject:
Mathematics, Mathematical Biology

This chapter discusses three approaches for analyzing qualitative properties of the dynamics of genetic regulatory networks, based on increasingly-abstract modeling formalisms: discrete abstractions ... More


Mediations of Gaia: Ecology and Epistemology from Gregory Boteson and Felix Guattari to Avatar

Bruce Clarke

in Neocybernetics and Narrative

Published in print:
2014
Published Online:
August 2015
ISBN:
9780816691005
eISBN:
9781452949406
Item type:
chapter
Publisher:
University of Minnesota Press
DOI:
10.5749/minnesota/9780816691005.003.0005
Subject:
Literature, Film, Media, and Cultural Studies

This chapter analyzes the theory of metabiotic autopoietic systems back to biotic autopoiesis and its subsequent developments, and towards the Gaia hypothesis. The theories of cognition from the ... More


The origins of evolutionary innovation

Andreas Wagner

in The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems

Published in print:
2011
Published Online:
December 2013
ISBN:
9780199692590
eISBN:
9780191774829
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199692590.003.0095
Subject:
Biology, Evolutionary Biology / Genetics

This chapter summarizes key material from the previous chapters, highlights these similarities, and points out how they affect the ability to innovate. The preceding chapters examined three very ... More


The Need for a Universal Definition of Life in Twenty-first-century Biology

Kepa Ruiz-Mirazo and Alvaro Moreno

in Information and Living Systems: Philosophical and Scientific Perspectives

Published in print:
2011
Published Online:
August 2013
ISBN:
9780262201742
eISBN:
9780262295246
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262201742.003.0002
Subject:
Philosophy, Philosophy of Science

This chapter works on the problem of the definition of life as a way to clarify and organize the achievements made in biology thus far, as well as to indicate the challenges that remain. Some ... More


System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

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 ... More


Varieties of Biological Information

Daniel Cloud

in The Domestication of Language: Cultural Evolution and the Uniqueness of the Human Animal

Published in print:
2014
Published Online:
November 2015
ISBN:
9780231167925
eISBN:
9780231538282
Item type:
chapter
Publisher:
Columbia University Press
DOI:
10.7312/columbia/9780231167925.003.0004
Subject:
Linguistics, Psycholinguistics / Neurolinguistics / Cognitive Linguistics

This chapter examines information and information processing in biological systems. Information processing of fairly complex kinds is fundamental to life. Cells seem to have recognizable memory ... More


Ansatz for Dynamical Hierarchies

Steen Rasmussen, Nils A. Baas, Bernd Mayer, and Martin Nillson

in Emergence: Contemporary Readings in Philosophy and Science

Published in print:
2008
Published Online:
August 2013
ISBN:
9780262026215
eISBN:
9780262268011
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262026215.003.0020
Subject:
Philosophy, Philosophy of Science

This chapter discusses the dynamical hierarchies in biological systems and molecular systems as well as higher-order dynamical hierarchies. In biological systems, hierarchies with multiple ... More


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