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Artificial Chemistries

Artificial Chemistries

Wolfgang Banzhaf
Lidia Yamamoto
Copyright Date: 2015
Published by: MIT Press
Pages: 576
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  • Book Info
    Artificial Chemistries
    Book Description:

    The field of Artificial Life (ALife) is now firmly established in the scientific world, but it has yet to achieve one of its original goals: an understanding of the emergence of life on Earth. The new field of Artificial Chemistries draws from chemistry, biology, computer science, mathematics, and other disciplines to work toward that goal. For if, as it has been argued, life emerged from primitive, prebiotic forms of self-organization, then studying models of chemical reaction systems could bring ALife closer to understanding the origins of life. In Artificial Chemistries (ACs), the emphasis is on creating new interactions rather than new materials. The results can be found both in the virtual world, in certain multiagent systems, and in the physical world, in new (artificial) reaction systems. This book offers an introduction to the fundamental concepts of ACs, covering both theory and practical applications.After a general overview of the field and its methodology, the book reviews important aspects of biology, including basic mechanisms of evolution; discusses examples of ACs drawn from the literature; considers fundamental questions of how order can emerge, emphasizing the concept of chemical organization (a closed and self-maintaining set of chemicals); and surveys a range of applications, which include computing, systems modeling in biology, and synthetic life. An appendix provides a Python toolkit for implementing ACs.

    eISBN: 978-0-262-32946-0
    Subjects: Chemistry, Biological Sciences

Table of Contents

  1. Front Matter
    (pp. i-vi)
  2. Table of Contents
    (pp. vii-x)
  3. Preface
    (pp. xi-xvi)
    Wolfgang Banzhaf and Lidia Yamamoto
  4. I Foundations

    • Chapter 1 Introduction
      (pp. 3-10)

      The study of Artificial Chemistries (ACs) originated from the efforts to understand the origins of life. Similarly to how Artificial Life studies models of “life as it could be,” artificial chemistries propose and study various models of chemical reactions as they could be imagined. In real chemistry, reactions happen when a set of molecules (the reactants) come into contact in such a way that some of the bonds between their atoms are broken and other bonds are formed, rearranging the atoms into the final products of the reaction. There are a vast number of different ways to rearrange atoms into...

    • Chapter 2 Basic Concepts of Artificial Chemistries
      (pp. 11-44)

      Before we can discuss the general structure of an artificial chemistry, we have to set the stage for this discussion by addressing two topics that together constitute the pillars of any artificial chemistry: the first one is a topic of very broad relevance to all of science and engineering, a topic fraught with misunderstandings: modeling and simulation. The second pillar is the topic of real chemistry, which is used as a source of inspiration for artificial chemistries, or as the target system to be modeled. In the first section of this chapter, we will therefore address the principles behind modeling...

    • Chapter 3 The Matrix Chemistry as an Example
      (pp. 45-62)

      This chapter discusses in depth a more complex example of an artificial chemistry, an algorithmic chemistry. In fact, it is an entire class of systems that can be treated in a similar way. The matrix chemistry is a system that was devised some time ago [63] to explore fundamental aspects of artificial chemistries in a simple abstract system. Despite its simplicity, the matrix chemistry provides sufficient richness in interactions to exemplify and discuss a number of important AC features. Its investigation was originally inspired by the application of genetic algorithms [703], [395] to problems of combinatorial optimization. It studies a...

    • Chapter 4 Computing Chemical Reactions
      (pp. 63-74)

      In chapter 2, the elements of an artificial chemistry were introduced: the set of moleculesS, the set of reaction rulesR, and the reactor algorithmA. A few reaction algorithms were then briefly described or just enumerated. In this chapter we will examine reactor algorithms in more detail. Before going any deeper in the realm of artificial chemistries, a look at the underlying reality and its description in real chemistry is in order.

      Chemical reactions are fundamentally interactions of material objects. Chemistry has, for centuries, heavily relied on the experimental scientific method to learn from chemical reality in our...

  5. II Life and Evolution

    • Chapter 5 The Chemistry of Life
      (pp. 77-110)

      Artificial chemistries stand to Artificial Life as chemistry stands to biology. The link between chemistry and biology is also intimately related to the origin of life from inanimate matter. The urge to understand the origin of life and the essence of the phenomenon of life was among the main motivations of Artificial Life that gave birth to Artificial Chemistry. A significant amount of the literature in Artificial Life and Artificial Chemistry can be truly understood only in the context of this long quest for the truth behind the organization of living beings. This is why the present chapter is devoted...

    • Chapter 6 The Essence of Life
      (pp. 111-138)

      The basic atoms of life (carbon, hydrogen, oxygen, and nitrogen) are everywhere. They are among the most common and cheapest chemical elements found on Earth. And yet, mixing them all together in a container does not result in anything near organic. The key to life is the way these atoms can form basic organic building blocks, and then how these building blocks can be combined into highly organized complex structures.

      The organization of current life forms is very complex indeed. How does such complexity emerge? Would it be possible to reduce it to the bare essential? Would it be possible...

    • Chapter 7 Evolution
      (pp. 139-158)

      After having mentioned evolution several times in past chapters, in this chapter we can finally delve into the actual mechanism of Darwinian evolution, or evolution by natural selection: what evolution is, why and how evolution works, its strengths and limitations, and of course, its relation to ACs.

      Why should a book about artificial chemistries dedicate a full chapter to evolution? One answer is because ACs can facilitate the study and understanding of evolution, since evolutionary processes can be modeled with artificial chemistries. Moreover, ACs can help to shed new light on the origin of evolution. Indeed, one of the main...

    • Chapter 8 Complexity and Open-Ended Evolution
      (pp. 159-178)

      Despite the obvious power of natural evolution, so far artificial evolution has not yet been capable of displaying the full richness of natural evolution. Typically, artificial evolution tends to stagnate at some point, while natural evolution seems to always find a way to move forward. Critics of evolutionary theory often use such weakness as an argument in their quest to prove it false. However, to most experts in the field, this only shows that our understanding of evolutionary processes is still far from complete. Indeed, evolution is a complex stochastic process driven by feedback and influenced by several parameters. The...

  6. III Approaches to Artificial Chemistries

    • Chapter 9 Rewriting Systems
      (pp. 181-194)

      So far, we have only discussed a very special numerical example of an artificial chemistry in chapter 3. It is now time to widen the horizon and look at what kind of systems have been used in the literature to capture the essentials of ACs. The next three chapters are dedicated to that purpose.

      We will start with production or rewriting systems, a very general class of formal systems in mathematics, computer science and logic, in which rules for replacing formal (sub)structures with others are repeatedly applied. We shall see that these systems provide a broad basis for artificial chemistries...

    • Chapter 10 Automata and Machines
      (pp. 195-224)

      In this chapter we shall look at another class of systems that can be used for the realization of artificial chemistries. Historically, these systems have been among the earliest used for implementing ACs, because, among other things, they provide a level of analogy to real chemistry that is remarkable.

      Like a real machine, its abstraction is a manufacturing device. It takes input,I, and produces outputO, presumably consuming energy (or the equivalent in an abstract space). Thus, we can write the action of a machine or automatonMas

      M+IMʹ +I+O. (10.1)...

    • Chapter 11 Bio-inspired Artificial Chemistries
      (pp. 225-254)

      In this chapter we are looking at examples of artificial chemistries that are inspired by biological systems. Some chemistries in this category have already appeared in chapters 9 or 10, such as P systems (inspired by the organization of eukaryotic cells), Typogenetics (inspired by how enzymes operate on DNA strands), and Coreworld, Tierra, and Avida (inspired by biological evolution). However, various other bio-inspired ACs exist, many of which do not fit purely into the rewriting or automata categories. This chapter is devoted to a closer look at some of these chemistries.

      Bio-inspired ACs will generally result in very complex systems...

  7. IV Order Construction

    • Chapter 12 The Structure of Organizations
      (pp. 257-274)
      Pietro Speroni di Fenizio

      The termorganizationis widely used in the sciences and humanities, from the social sciences and economy to physics, chemistry, and computer science. In nearly all these areas,organizationhas a specific meaning, which is sufficient for qualitative statements on a system embedded in a specific context. Often further qualifications apply, such as in self-organization, an area of research that has become very active in the last decades [70]. However, once quantitative measurements are sought, an exact definition of organization is necessary.

      This chapter discusses theoretical concepts of a framework that is useful to define ”organization.” We will use precise...

    • Chapter 13 The Dynamics of Organizations
      (pp. 275-286)

      In the last chapter we learned what could constitute an organization and how we might, starting from a reaction table, derive the potential organizations of a reaction system. However, the situation is a bit more complicated than we dared to explain there, in that a few more conditions need to be fulfilled for a system to actually possess those structures that we call organizations.

      Essentially, we have to consider not only the static connections in the reaction graph but also the flow of material/energy/information through the graph as a very important criterion when examining organizations. This is what we shall...

    • Chapter 14 Self-Organization and Emergent Phenomena
      (pp. 287-306)

      Now that we have discussed the theory of organization to some degree, it is time to turn our attention to what has become a core concept of systems science: self-organization. In general terms, this refers to the ability of a class of systems to change their internal structure and/or their function in response to external circumstances. Elements of self-organizing systems are able to manipulate or organize other elements of the same system in a way that stabilizes either structure or function of the whole against external fluctuations. The process of self-organization is often achieved by growing the internal space-time complexity...

    • Chapter 15 Constructive Dynamical Systems
      (pp. 307-320)

      It has often been said that Charles Darwin, in his book on theOrigin of Species, aimed at one theme (the origin) but delivered on another (the mechanism of selection). Fontana and Buss, in their article [282] discuss this at greater length and choose the title of their contribution accordingly. The question not clearly answered by Darwin is how it is that new species emerge out of older ones, in a way similar to the process of new cells emerging out of previous ones in the cell division process of cell biology. Before the important event, only one cell was...

  8. V Applications

    • Chapter 16 Applications of Artificial Chemistries
      (pp. 323-344)

      Artificial Chemistries have been applied to a variety of domains, ranging from wet chemical computing to automated music composition. The present chapter is the first of part V of this book, covering various application domains of artificial chemistries. The current chapter discusses a selection of examples intended to be at the same time simple enough and illustrative of a broad range of AC application possibilities.

      The first AC example has taken inspiration from the world of bacteria, namely their chemical composition and behavior. Bacteria must be able to detect rapid changes in their environment and to adapt their metabolism to...

    • Chapter 17 Computing with Artificial Chemistries
      (pp. 345-372)

      A chemical reaction entails a transformation from one state (the collective state of the educts) to another (the products of the reaction). Computation also transforms states by processing input data into output results. Hence, chemistry can be seen as a natural model of computation and can be recruited for computational purposes. Throughout this book we have already seen some examples of algorithms implemented with artificial chemistries, such as decomposing numbers into primes (Chapter 2), or sorting numbers in parallel using Gamma or MGS (Chapter 9). In this chapter we will delve more deeply into the techniques for programming inspired by...

    • Chapter 18 Modeling Biological Systems
      (pp. 373-404)

      As abstract chemical systems, artificial chemistries find natural applicability in the modeling of biological systems. In this chapter we examine the role of artificial chemistries in this context. One of the strengths of ACs for modeling biology is their ability to abstract away from the biochemical details while retaining the constructive potential to deal with combinatorially complex models of biomolecules and their interactions. Such a level of resolution lies somewhere between fine-grain molecular modeling [499, 751] and more macroscopic models such as those based on differential equations and agent-based modeling [83, 711, 907].

      In chapter 2 we discussed modeling and...

    • Chapter 19 Wet Artificial Chemistries
      (pp. 405-438)

      In this chapter we will attempt an excursion into “wetland:” the world of synthetic biology and wet computersin vitroandin vivo. The nascent discipline of synthetic biology explores the idea that cells and even entire organisms can be reengineered and reprogrammed to perform specific functions. They might be even created from scratch out of laboratory chemicals. Natural cells and their components are also candidates for computing devices. In his bookWetware: A Computer in Every Living Cell, Bray defends the thesis that “living cells perform computations” and shows several examples, from proteins that behave like switches via genetic...

    • Chapter 20 Beyond Chemistry and Biology
      (pp. 439-448)

      This chapter is devoted to the discussion of some of the variety of models of artificial chemistries employed beyond chemistry and biology. First, we shall look at self-assembly and discover how it refers not only to molecular interactions but also to the interaction of macroscopic bodies. The laws governing self-assembly can be analogously applied and again show the prevalence of chemical kinetics. This is followed by a discussion of nuclear and particle physics reactions. Again, the collision of entities leads to changes in their collective constitution and this can be modeled using ACs. Even in economic and social systems, similar...

  9. VI Conclusions

    • Chapter 21 Summary and Perspectives
      (pp. 451-460)

      The field of artificial chemistry has developed substantially over the past several years. With the growth in the prowess of computer technology so grew the ability to perform simulations of fine-grained systems. From bulk matter to molecules to elementary particles, a whole range of material systems is now open for numerical studies in which to employ artificial chemistries. And not only the micro- and meso-scale of material entities is accessible to AC simulation, we have seen macro-scale examples, too, ranging from organisms to mechanical devices to economic and social entities.

      What all of these approaches have in common is the...

  10. Further Reading
    (pp. 461-462)
  11. Appendix: Setting up Your Own Artificial Chemistry System
    (pp. 465-480)
  12. Bibliography
    (pp. 481-530)
  13. Author Index
    (pp. 531-544)
  14. Subject Index
    (pp. 545-555)