Information and Living Systems

Information and Living Systems: Philosophical and Scientific Perspectives

George Terzis
Robert Arp
Copyright Date: 2011
Published by: MIT Press,
Pages: 464
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  • Book Info
    Information and Living Systems
    Book Description:

    Information shapes biological organization in fundamental ways and at every organizational level. Because organisms use information--including DNA codes, gene expression, and chemical signaling--to construct, maintain, repair, and replicate themselves, it would seem only natural to use information-related ideas in our attempts to understand the general nature of living systems, the causality by which they operate, the difference between living and inanimate matter, and the emergence, in some biological species, of cognition, emotion, and language. And yet philosophers and scientists have been slow to do so. This volume fills that gap. Information and Living Systems offers a collection of original chapters in which scientists and philosophers discuss the informational nature of biological organization at levels ranging from the genetic to the cognitive and linguistic.The chapters examine not only familiar information-related ideas intrinsic to the biological sciences but also broader information-theoretic perspectives used to interpret their significance. The contributors represent a range of disciplines, including anthropology, biology, chemistry, cognitive science, information theory, philosophy, psychology, and systems theory, thus demonstrating the deeply interdisciplinary nature of the volume's bioinformational theme.

    eISBN: 978-0-262-29524-6
    Subjects: Philosophy, General Science

Table of Contents

  1. Front Matter
    (pp. i-vi)
  2. Table of Contents
    (pp. vii-viii)
  3. Preface
    (pp. ix-x)
  4. Introduction
    (pp. xi-xliv)

    The idea of information has become increasingly important in our efforts to understand the nature of biological organization. It is now generally recognized that information-related ideas play a key role in characterizing life at every organizational level. Familiar examples of these ideas include: how DNA codes for specific amino-acid sequences, how gene expression shapes biological development, how chemical signaling enables the immune system to combat pathogens, and at the cognitive end of the biological continuum, how populations of neurons represent features of our environment. But although pervasive, the contribution that information-related ideas make to our understanding of these processes is...

  5. I The Definition of Life
    • 1 The Need for a Universal Definition of Life in Twenty-first-century Biology
      (pp. 3-24)
      Kepa Ruiz-Mirazo and Alvaro Moreno

      Twentieth-century biology was based on and shaped by the concept of the gene, thus yielding extraordinary results, like the development of molecular biology and the modern synthesis of evolutionary theory (Keller 2000). The idea that processes in biological systems could be explained solely in terms of the properties of their molecular components was so prominent that it overshadowed the idea that there is something else relevant for biology to do, namely, to explain the complex dynamicintegrationof those components into functional units—that is, living cells. This reductionist approach concealed the organicist currents of thought that, having emerged from...

    • 2 Energy Coupling
      (pp. 25-52)
      Yaşar Demirel

      As opposed to nonliving systems, living systems can reproduce as well as collect, process, and exchange information in order to control and direct energy and matter they receive from their environments. Living systems extract free energy from the sun, store it, and use it for sorting and motile activities. Chloroplasts use energy to initiate electron transfer cycles and proton gradients to produce adenosine triphosphate (ATP) and carbohydrates in photosynthesis. Mitochondria use carbohydrates as food molecules to create electron transfer cycles and proton gradients to produce ATP and carbon dioxide in oxidative phosphorylation. Feeding carbon dioxide back to photosynthesis completes the...

  6. II Information and Biological Organization
    • 3 Bioinformation as a Triadic Relation
      (pp. 55-90)
      Alfredo Marcos

      Information is seen today not as a unitary concept, but as a family of concepts whose members lack any clear interconnection. The relationships of this family’s members with neighboring notions, such as knowledge, form, entropy, correlation, probability, meaning, order, organization, and complexity, also require clarification. Furthermore, measurements of information are normally interpreted as gauges of structural complexity, correlation, thermodynamic order, or potential information, and as such, are unable to discriminate biological functionality. The clarification of the concept of information and its relationships with other surrounding notions, along with the development of a measure of functional information are, therefore, important tasks...

    • 4 The Biosemiotic Approach in Biology: Theoretical Bases and Applied Models
      (pp. 91-130)
      João Queiroz, Claus Emmeche, Kalevi Kull and Charbel El-Hani

      Biosemiotics is a growing field that investigates semiotic processes in the living realm in an attempt to combine the findings of the biological sciences and semiotics. Semiotic processes are more or less what biologists have typically referred to as “signals,” “codes,” and “information processing” in biosystems, but these processes are here understood under the more general notion ofsemiosis, that is, the production, action, and interpretation of signs. Thus, biosemiotics can be seen as biology interpreted as a study of living sign systems—which also means that semiosis or sign process can be seen as the very nature of life...

    • 5 Problem Solving in the Life Cycles of Multicellular Organisms: Immunology and Cancer
      (pp. 131-156)
      Niall Shanks and Rebecca A. Pyles

      The aim of the present inquiry is to incorporate our current understanding of information processing and problem solving in biological systems into an evolutionary perspective. Because our discussion centers on biological phenomena in multicellular organisms, and those especially relevant to human medicine, we also present perspectives most commonly assigned to the field of Darwinian medicine. We present two detailed case studies concerning: (1) adaptive immunity, whereby the immune system has to process information to solve problems in the face of host-parasite coevolution, and (2) the dynamics of cancer, whereby lineages of cancer cells evolve adaptations in a complex and hostile...

    • 6 The Informational Nature of Biological Causality
      (pp. 157-176)
      Alvaro Moreno and Kepa Ruiz-Mirazo

      Biological entities constitute highly complex systems. Since Darwin, this complexity has been thought to result from a long-term historical and collective process that goes far beyond the ontogenetic trajectories of individual living beings. In that framework, one in which biological activity takes place in a physically limited environment but conveys a spatial and temporal dimension larger than that of a single organism, natural selection would explain how the diversity and complexity of living phenomena may increase over time. Furthermore, this Darwinian evolutionary process, which involves a whole population of systems undergoing many subsequent reproductive cycles, seems to not have a...

    • 7 The Self-construction of a Living Organism
      (pp. 177-204)
      Natalia López-Moratalla and María Cerezo

      Recent developments in genetics and developmental biology have shown that the role of genetic information in living organisms is, in one sense, stronger than had been thought and, in another sense, weaker. Insofar as the living organism has certain material constituents—namely DNA, whose sequence of nucleotides (DNAprimary structure, orgeneticinformation) can be interpreted as a kind of sign of something (be this a synthesis of proteins or particular features of the organism)—it seems beyond question that the genome is informative (Barbieri 2003; Maynard Smith 2000). Epigenetics has further amplified and limited this role. It has amplified...

    • 8 Plasticity and Complexity in Biology: Topological Organization, Regulatory Protein Networks, and Mechanisms of Genetic Expression
      (pp. 205-250)
      Luciano Boi

      This discussion is aimed first at studying some important aspects of the plasticity and complexity of biological systems and their links. We shall further investigate the relationship between the topological organization and dynamics of chromatin and chromosome, the regulatory proteins networks, and the mechanisms of genetic expression. Our final goal is to show the need for new scientific and epistemological approaches to the life sciences. In this respect, we think that in the near future, research in biology has to shift drastically from a genetic and molecular approach to an epigenetic and organismal approach, particularly by studying the network of...

  7. III Information and the Biology of Cognition, Value, and Language
    • 9 Decision Making in the Economy of Nature: Value as Information
      (pp. 253-288)
      Benoit Hardy-Vallée

      Cognition, to use Reuven Dukas’s formula, is the set of “neuronal processes concerned with the acquisition, retention, and use of information” (Dukas 2004, 347). Decision making is one of the principalusesof that information. Classically, decision making is not a topic of discussion in biology and philosophy of biology. The analysis and study of decision making is usually left to philosophy of mind, economics and psychology (see Hardy-Vallée 2007, forthcoming). Philosophers are mostly concerned with the normative features of decisions, that is, what makes a decision rational or not. In philosophy of mind, the standard conception of decision making...

    • 10 Information Theory and Perception: The Role of Constraints, and What Do We Maximize Information About?
      (pp. 289-308)
      Roland Baddeley, Benjamin Vincent and David Attewell

      Because human and nonhuman primates are highly visual animals, an important step in understanding how their brains operate is to understand how they see: that is, how they transform the structured, colored, and dynamic pattern of light surrounding them into knowledge about the world they live in. Over the last twenty years, a number of problems associated with understanding vision have used information-theoretic techniques to help us gain insight into perception (Shannon 1948). This chapter will describe, in a biased way, one particular strand of this work: how information theory has been used to shed light on the processes and...

    • 11 Attention, Information, and Epistemic Perception
      (pp. 309-352)
      Nicolas J. Bullot

      Attention became a topic studied in experimental psychology by the end of the nineteenth century. With the subsequent development of psychology, interdisciplinary research on attention became an integral part of the cognitive and medical sciences (Posner and Raichle 1994; Parasuraman 1998; Wright 1998; Braun, Koch, and Davis 2001; Handy, Hopfinger, and Mangun 2001). Meanwhile, attention continues to raise a wide range of philosophical questions concerning, for example, sensory-motor control, perceptual reference, language understanding, social intentionality, and the neural correlates of consciousness. This chapter focuses on a question that is fundamental to bridging the gap between epistemology and biology: what is...

    • 12 Biolinguistics and Information
      (pp. 353-370)
      Cedric Boeckx and Juan Uriagereka

      Modern (theoretical) linguistics was born half a century ago in the midst of what is often called the cognitive revolution. Noam Chomsky (1956, 1957), Morris Halle (1995, 2002), Eric Lenneberg (1967), and others distanced themselves from the then-dominant behaviorist paradigm, and reached back to earlier philosophical concerns, using the faculty of language as “a mirror to the mind.” Rather than as a list of behaviors or a communication mechanism, language was seen as an organ of the mind, a key to understanding mental life. If psychology is defined as the science of mental life, then linguistics animated by rationalist concerns...

    • 13 The Biology of Personality
      (pp. 371-406)
      Aurelio José Figueredo, W. Jake Jacobs, Sarah B. Burger, Paul R. Gladden and Sally G. Olderbak

      The biology of personality can be described at multiple, complementary levels of analysis:descriptive, behavioral-genetic, neuroanatomical, neurochemical, situational,andbehavioral-ecological. None of these individual levels of analysis separately presents a complete picture of the biology of personality, but we provide a multilayered perspective by presenting a theoretically coherent andconsilient(Wilson 1998), vertical integration of these various levels, linking proximate with ultimate levels of causation. Each of these levels of analysis can be thought of as members of a constitutive hierarchy, as described by Ernst Mayr:

      In such a hierarchy the members of a lower level, let us say tissues,...

  8. Contributors
    (pp. 407-408)
  9. Index
    (pp. 409-414)