Computational methods such as computer simulations, Monte Carlo methods, and agent-based modeling have become the dominant techniques in many areas of science. Extending Ourselves contains the first systematic philosophical account of these new methods, and how they require a different approach to scientific method. Paul Humphreys draws a parallel between the ways in which such computational methods have enhanced our abilities to mathematically model the world, and the more familiar ways in which scientific instruments have expanded our access to the (...) empirical world. This expansion forms the basis for a new kind of empiricism, better suited to the needs of science than the older anthropocentric forms of empiricism. Human abilities are no longer the ultimate standard of epistemological correctness.Humphreys also includes arguments for the primacy of properties rather than objects, the need to consider technological constraints when appraising scientific methods, and a detailed account of how the path from computational template to scientific application is constructed. This last feature allows us to hold a form of selective realism in which anti-realist arguments based on formal reconstructions of theories can be avoided. One important consequence of the rise of computational methods is that the traditional organization of the sciences is being replaced by an organization founded on computational templates.Extending Ourselves will be of interest to philosophers of science, epistemologists, and to anyone interested in the role played by computers in modern science. (shrink)

Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that self-organization plays an (...) important role in the emergence of life itself and may play as fundamental a role in shaping life's subsequent evolution as does the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt remain poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biologicalscience itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences. (shrink)

The fitness of any evolutionary unit can be understood in terms of its two basic components: fecundity (reproduction) and viability (survival). Trade-offs between these fitness components drive the evolution of life-history traits in extant multicellular organisms. We argue that these trade-offs gain special significance during the transition from unicellular to multicellular life. In particular, the evolution of germ–soma specialization and the emergence of individuality at the cell group (or organism) level are also consequences of trade-offs between the two basic fitness (...) components, or so we argue using a multilevel selection approach. During the origin of multicellularity, we study how the group trade-offs between viability and fecundity are initially determined by the cell level trade-offs, but as the transition proceeds, the fitness trade-offs at the group level depart from those at the cell level. We predict that these trade-offs begin with concave curvature in single-celled organisms but become increasingly convex as group size increases in multicellular organisms. We argue that the increasingly convex curvature of the trade-off function is driven by the cost of reproduction which increases as group size increases. We consider aspects of the biology of the volvocine green algae – which contain both unicellular and multicellular members – to illustrate the principles and conclusions discussed. (shrink)

Recently, biologists and computer scientists who advocate the "strong thesis of artificial life" have argued that the distinction between life and nonlife is important and that certain computer software entities could be alive in the same sense as biological entities. These arguments have been challenged by Sober (1991). I address some of the questions about the rational reconstruction of biology that are suggested by these arguments: What is the relation between life and the "signs of life"? What work (if any) (...) might the concept of "life" (over and above the "signs of life") perform in biology? What turns on scientific disputes over the utility of this concept? To defend my answers to these questions, I compare "life" to certain other concepts used in science, and I examine historical episodes in which an entity's vitality was invoked to explain certain phenomena. I try to understand how these explanations could be illuminating even though they are not accompanied by any reductive definition of "life.". (shrink)

Weak emergence has been offered as an explication of the ubiquitous notion of emergence used in complexity science (Bedau 1997). After outlining the problem of emergence and comparing weak emergence with the two other main objectivist approaches to emergence, this paper explains a version of weak emergence and illustrates it with cellular automata. Then it explains the sort of downward causation and explanatory autonomy involved in weak emergence.

Weak emergence has been offered as an explication of the ubiquitous notion of emergence used m complexity science After outlining the problem of emergence and comparing weak emergence with the two other weak objectivist approaches to emergence, the paper explains a version of weak emergence and illustrates at with cellular automata Then it explains the sort of downward causation and explanatory autonomy involved m weak emergence.

In Darwinism's Struggle for Survival Jean Gayon offers a philosophical interpretation of the history of theoretical Darwinism. He begins by examining the different forms taken by the hypothesis of natural selection in the nineteenth century and the major difficulties which it encountered, particularly with regard to its compatibility with the theory of heredity. He then shows how these difficulties were overcome during the seventy years which followed the publication of Darwin's Origin of Species, and he concludes by analysing the major (...) features of the genetic theory of natural selection, as it developed from 1920 to 1960. This rich and wide-ranging study will appeal to philosophers and historians of science and to evolutionary biologists. (shrink)

A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving (...) complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection. (shrink)

I investigate the relationship between adaptation, as defined in evolutionary theory through natural selection, and the concept of emergence. I argue that there is an essential correlation between the former, and “emergence” defined in the field of algorithmic simulations. I first show that the computational concept of emergence (in terms of incompressible simulation) can be correlated with a causal criterion of emergence (in terms of the specificity of the explanation of global patterns). On this ground, I argue that emergence in (...) general involves some sort of selective processes. Finally, I show that a second criterion, concerning novel explanatory regularities following the emergence of a pattern, captures the robustness of emergence displayed by some cases of emergence (according to the first criterion). Emergent processes fulfilling both criteria are therefore exemplified in evolutionary biology by some so-called “innovations”, and mostly by the new units of fitness or new kinds of adaptations (like sexual reproduction, multicellular organisms, cells, societies) sometimes called “major transitions in evolution”, that recent research programs (Maynard-Smith and Szathmary 1995 ; Michod 1999 ) aims at explaining. (shrink)

Systems involving many interacting variables are at the heart of the natural and social sciences. Causal language is pervasive in the analysis of such systems, especially when insight into their behavior is translated into policy decisions. This is exemplified by economics, but to an increasing extent also by biology, due to the advent of sophisticated tools to identify the genetic basis of many diseases. It is argued here that a regularity notion of causality can only be meaningfully defined for systems (...) with linear interactions among their variables. For the vastly more important class of nonlinear systems, no such notion is likely to exist. This thesis is developed with examples of dynamical systems taken mostly from mathematical biology. It is discussed with particular reference to the problem of causal inference in complex genetic systems, systems for which often only statistical characterizations exist. (shrink)

Arguments for or against a trend in the evolution of complexity are weakened by the lack of an unambiguous definition of complexity. Such definitions abound for both dynamical systems and biological organisms, but have drawbacks of either a conceptual or a practical nature. Physical complexity, a measure based on automata theory and information theory, is a simple and intuitive measure of the amount of information that an organism stores, in its genome, about the environment in which it evolves. It is (...) argued that physical complexity must increase in molecular evolution of asexual organisms in a single niche if the environment does not change, due to natural selection. It is possible that complexity decreases in co‐evolving systems as well as at high mutation rates, in sexual populations, and in time‐dependent landscapes. However, it is reasoned that these factors usually help, rather than hinder, the evolution of complexity, and that a theory of physical complexity for co‐evolving species will reveal an overall trend towards higher complexity in biological evolution. BioEssays 24:1085–1094, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

It is often claimed that artificial society simulations contribute to the explanation of social phenomena. At the hand of a particular example, this paper argues that artificial societies often cannot provide full explanations, because their models are not or cannot be validated. Despite that, many feel that such simulations somehow contribute to our understanding. This paper tries to clarify this intuition by investigating whether artificial societies provide potential explanations. It is shown that these potential explanations, if they contribute to our (...) understanding, considerably differ from potential causal explanations. Instead of possible causal histories, simulations offer possible functional analyses of the explanandum . The paper discusses how these two kinds explanatory strategies differ, and how potential functional explanations can be appraised. (shrink)

To surmount the notorious difficulties of defining life, we should evaluate theories of life not by whether they provide necessary and sufficient conditions for our current preconceptions about life but by how well they explain living phenomena and how satisfactorily they resolve puzzles about life. On these grounds, the theory of life as supple adaptation (Bedau 1996) gets support from its natural and compelling resolutions of the following four puzzles: (1) How are different forms of life at different levels of (...) the vital hierarchy related? (2) Is there a continuum between life and non-life? (3) Does life essentially concern a living entity’s material composition or its form? (4) Are life and mind intrinsically connected? (shrink)