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Introductory Concepts

Domitilla Del Vecchio and Richard M. Murray

in Biomolecular Feedback Systems

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

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 feedback systems. It begins with a discussion of the role of modeling, analysis, and feedback in biological systems. This is followed by a short review of key concepts and tools from control and dynamical systems theory, which is intended to provide insight into the main methodology described in this volume. Finally, this chapter gives another brief introduction—this time to the field of synthetic biology, which is the primary topic of the latter portion of this book.Less

General Features of Life

Gennaro Auletta

in Cognitive Biology: Dealing with Information from Bacteria to Minds

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.

From Bacteria to Belief: Immunity and Security

Luis P. Villarreal

in Natural Security: A Darwinian Approach to a Dangerous World

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

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 prokaryotes, such as bacteria. It outlines the evolution of biological models of group identity and immunity and presents a thesis that links biological identity systems to security systems. Security, immunity, and group identity are presented as highly related concepts, all of which depend on an ancient and enduring strategy that uses addiction modules. Human social identity, the source of many security concerns, has retained these basic biological strategies.Less

The Work of Biological Individuality: Concepts and Contexts

Scott Lidgard and Lynn K. Nyhart

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

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

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 years. Using the notion of a dynamic problem space to explore biological, historical, and philosophical aspects of biological individuality, we argue that the work of biological individuality concepts must be understood contextually. These concepts are contextualized by specific research problems, biological systems, and epistemic goals; by different disciplinary norms; and by change over time. Concepts also address different categories of problems involving individuation, hierarchies or levels, temporal continuity or change, and what does or does not constitute an individual. To move our understanding of biological individuality forward productively, we recast it as a broad, stable, and growing domain of problems that each merit investigation in its own right, for which no single definition of individuality will suffice.Less

Model Systems, Model Organisms

Rowland H. Davis

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

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

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 Renaissance yielded enlightenment, the classification of organisms and a study of their structures embodied a new attempt to subdue the mystery of life. The effort was satisfying in confirming the systematic intentions of the designer. But as the last millennium progressed, the urge simply to recognize and sort plants and animals gave way to an ambition to understand their origins, functions, and diversity. Detached from constraints of authority by the examples of Galileo and Newton, the early explorers of the living domain began to ask empirical questions buried for centuries, latent in the human imagination. This chapter explores the choice and use of organisms in answering these questions. The organisms now living on earth are so diverse that one must ask how biologists made such choices. It looks at the organisms that brought biology to the beginning of the 20th century, when particular models began to guide experimental research and for a time limited our appreciation of organismic diversity. In doing so, it shows how very recent our understanding of living things really is, and why we saw such an acceleration of biological research in the 20th century.Less

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

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

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 of cellular complexity in more biological detail. It attempts to distinguish the type of complexity present in biological and physical systems by focusing on functional and organizational principles that underlie this complexity at a more abstract level. Next, it explores robustness as a concept for understanding biological function and behavior. This is followed by a discussion of two biological example systems, namely central metabolism and circadian clocks. These examples explain how and why robustness can help in modeling cellular complexity.Less

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

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

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 of chromatin and chromosome, the regulatory proteins networks, and the mechanisms of genetic expression are also investigated further in the following sections. The ultimate goal is to show the need for new scientific and epistemological approaches to the life sciences. In this respect, it is argued that, in the near future, research in biology must shift drastically from a genetic and molecular approach to an epigenetic and organismal approach, particularly by studying the network of interactions among gene pathways, the formation and dynamics of chromatin structures, and how environmental conditions may affect the response and evolution of cells and living systems.Less

On Modules and Modularity

Zoltan Szallasi, Vipul Periwal, and Jörg Stelling

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

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 complexity of biological systems requires unifying, simplifying concepts that might allow a predictive understanding of their functioning. Suggestions for such concepts include “modularity” along with robustness, discussed in Chapter 2. This chapter considers the existence of modules in biology, and the utility of this concept. Specifically, it discusses the concept of modules in other biological disciplines; the concept of modularity in systems biology; and definition of modules for dynamic networks.Less

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

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

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 purposes and implications of modeling; the different kinds of models; and sensitivity analysis.Less

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

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

This chapter discusses three approaches for analyzing qualitative properties of the dynamics of genetic regulatory networks, based on increasingly-abstract modeling formalisms: discrete abstractions of differential equations, Boolean networks, and graphs. Whereas the first two approaches use models that explicitly describe the dynamics of the system, the third approach is based on the assumption that an analysis of the structure of the system provides useful insights into its dynamics. The approaches are illustrated by means of a simple two-gene network and an example of their application to real biological systems.Less

Bodily Parts in the Structure-Function Dialectic

Ingo Brigandt

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

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

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 areas of biology. While structures are obvious bodily parts and structure and function have often been seen as antagonistic principles in the study of organismal organization, my tenet is that structures and functions are on a par. I articulate a notion of function (functions as activities), according to which functions are bodily parts just as structures are. Recognizing part-whole relations among an organism’s various structures and functions permits fruitful investigation and multilevel explanation of organismal properties and functioning, across both developmental and evolutionary time. I show how my perspective clarifies debates surrounding homology and evolutionary novelty that stem from an alleged structure-function dichotomy.Less

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

Bruce Clarke

in Neocybernetics and Narrative

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

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 previous chapters are rooted in the cellular sentience proposed by biological systems theory and validated by contemporary molecular biology and microbial ecology, all of which resulted in a corresponding conception of the biosphere. The chapter begins with tracing the history of the word ecology, citing Gregory Bateson’s collection of professional papers, Steps to an Ecology of Mind, as an influential work of the natural concept towards “an ecology of ideas.” Felix Guattari formulated his own ecological theory in The Three Ecologies, which can be juxtaposed to that of Bateson’s. The chapter explores Bruno Latour’s research on the film Avatar and its application of Gaian science, aka Earth system science.Less

The origins of evolutionary innovation

Andreas Wagner

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

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

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 different classes of biological systems. These are large metabolic networks, biological circuits that regulate gene activity, as well as protein and RNA molecules. Most evolutionary innovations arise through changes in these systems. Any theory of innovation thus needs to apply to systems as different as these. At first sight, this may seem impossible, precisely because these systems are so different. But on a deeper level, they also share important similarities. These similarities can help us understand the ability of living things to innovate.Less

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

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

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 authors, such as Cleland and Chyba, maintain that the current situation is not ripe enough and that it is necessary to wait for a general theory of biology before a proper definition of life can be successfully articulated; however, the work of synthesis needed to generate and defend such a definition could actually help form the basis for a general theory of biological systems. The chapter elaborates and defends a concrete proposal derived from the analysis of conditions and mechanisms underlying minimal forms of organization. This proposal is not a final destination, but serves as a launching pad that will eventually bring us closer to one.Less

Ansatz for Dynamical Hierarchies

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

in Emergence: Contemporary Readings in Philosophy and 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

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 functionalities at different scales can be found everywhere. On the molecular level, novel functionalities can arise in at least two ways: by assembly; and by evolution. The properties associated with each level are generated by the collective dynamics of the elements in these dynamical hierarchies; however, here arises the problem of creating a formal framework for consistently describing such hierarchical systems, with a procedure for moving between levels. It is probably necessary to embrace assembly and evolution as two complementary and equally important aspects of how to generate bio-complexity that can account for the generation and prevalence of dynamical hierarchies in living systems.Less

Varieties of Biological Information

Daniel Cloud

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

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

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 molecules for storing information, as well as molecules that are used for signaling. There is often machinery for recombining, permuting, or otherwise manipulating stored information in organized and elaborate ways. There is also machinery or some other provision for filtering out noise. All these are components that any physically realized information-processing device would need. The chapter asks: How should we think about this sort of biological information? Is it a real part of nature, or just something we humans anthropomorphically project onto the brute physical complexity of the real world? It also considers birdsong, particularly the gap in complexity between birdsong and human speech.Less