This collection of specially commissioned essays puts top scholars head to head to debate the central issues in the lively and fast growing field of philosophy ...

In this paper, I investigate the nature of a priori biological laws in connection with the idea that laws must be empirical. I argue that the epistemic functions of a priori biological laws in biology are the same as those of empirical laws in physics. Thus, the requirement that laws be empirical is idle in connection with how laws operate in science. This result presents a choice between sticking with an unmotivated philosophical requirement and taking the functional equivalence of laws (...) seriously and modifying our philosophical account. I favor the latter. (shrink)

Abstract: In this paper, my main objective is to investigate the nature of a priori biological laws in connection with the idea that laws must be empirical. I argue that functions of so-called a priori biological laws in biological sciences are the same as those of empirical physical laws. Thus, the requirement of being empirical makes no difference how laws operate in sciences. This result presents us a choice between sticking with a philosophical requirement of laws being empirical or taking (...) functional equivalences of laws seriously and modify our philosophical accounts of laws. I favor the latter. The paper consists of 4 sections. In section 1, I define the problem and I briefly explain my strategy in addressing it. In section 2, I discuss the relation between explanation and laws. In section 3, I compare a priori biological laws with some physical laws and I argue that their functions are the same in sciences to which they belong. In section 4, I discuss the implications of my discussions in sections 2 and 3 and I argue that the requirement of empirical is too strong. (shrink)

Biological knowledge does not fit the image of science that philosophers have developed. Many argue that biology has no laws. Here I criticize standard normative accounts of law and defend an alternative, pragmatic approach. I argue that a multidimensional conceptual framework should replace the standard dichotomous law/accident distinction in order to display important differences in the kinds of causal structure found in nature and the corresponding scientific representations of those structures. To this end I explore the dimensions of stability, strength, (...) and degree of abstraction that characterize the variety of scientific knowledge claims found in biology and other sciences. (shrink)

The primary purpose of this paper is to argue that biologists should stop citing Karl Popper on what a genuinely scientific theory is. Various ways in which biologists cite Popper on this matter are surveyed, including the use of Popper to settle debates on methodology in phylogenetic systematics. It is then argued that the received view on Popper—namely, that a genuinely scientific theory is an empirically falsifiable one—is seriously mistaken, that Popper’s real view was that genuinely scientific theories have the (...) form of statements of laws of nature. It is then argued that biology arguably has no genuine laws of its own. In place of Popperian falsifiability, it is suggested that a cluster class epistemic values approach (which subsumes empirical falsifiability) is the best solution to the demarcation problem between genuine science and pseudo- or non-science. (shrink)

This paper develops an account of explanation in biology which does not involve appeal to laws of nature, at least as traditionally conceived. Explanatory generalizations in biology must satisfy a requirement that I call invariance, but need not satisfy most of the other standard criteria for lawfulness. Once this point is recognized, there is little motivation for regarding such generalizations as laws of nature. Some of the differences between invariance and the related notions of stability and resiliency, due respectively to (...) Sandra Mitchell and Brian Skyrms, are explored. (shrink)

This article considers the question of embodiment in relation to gender and whether there are models of artificial intelligence (AI) which can enrol a concept of gender in their design. A central concern for feminist epistemology is the role of the body in the making of knowledge. I consider how this may inform a critique of the AI project and the related area of artificial life (A-Life), the latter area being of most interest in this paper. I explore briefly the (...) tensions between the treatment of the body in different branches of feminist theory, especially the tensions between the approaches of feminist sociology and feminist philosophy. I explore the ways in which writing from category theory and anthropological phenomenology offers rich suggestions as to how the body has been left out of objectivist accounts of epistemology, but struggles to offer an account of why. In its analysis of the links between women, knowledge and the body, feminist revisions of epistemology offer a more convincing why. This is explored briefly through a critique of symbolic AI, and more substantially through the problem of embodiment in artificial life. (shrink)

From the legendary inventor Daedalus to Goethe's tragic Faust, from the automata-making magicians of E.T.A Hoffmann to Mary Shelley's Victor Frankenstein – ...

Paper published on author's website available at http://www.garybanham.net/PAPERS_files/Artificial%20Life%20and%20the%20Inhuman%20Condition.pdf.

Contemporary artificial life (also known as “ALife”) is an interdisciplinary study of life and life-like processes. Its two most important qualities are that it focuses on the essential rather than the contingent features of living systems and that it attempts to understand living systems by artificially synthesizing extremely simple forms of them. These two qualities are connected. By synthesizing simple systems that are very life-like and yet very unfamiliar, artificial life constructively explores the boundaries of what is possible for life. (...) At the moment, artificial life uses three different kinds of synthetic methods. “Soft” artificial life creates computer simulations or other purely digital constructions that exhibit life-like behavior. “Hard” artificial life produces hardware implementations of life-like systems. “Wet” artifi- cial life involves the creation of life-like systems in a laboratory using biochemical materials. (shrink)

The aim of this chapter is to show how the technological research activity called “artificial life” is shedding new light on human creativity. Artificial life aims to understanding the fundamental behavior of life-like systems by synthesizing that behavior in artificial systems (more on artificial life below). One of the most interesting behaviors of living systems is their creativity. Biological creativity can be found in both individual living organisms and in the whole biosphere—the entire interconnected system comprised of all forms of (...) life—but I will focus in this chapter on the biological creativity exhibited by the evolutionary process. This is the creativity that enabled the earliest simple life forms to spontaneously evolve into the incredibly rich and beautiful diversity of life that now surrounds us. This diversity of life includes the most complex adaptive and intelligent systems in the known universe. This is an amazingly powerful spontaneous creation process, indeed. I will refer to it as hyper-creativity to call attention to the way in which it produces qualitatively new and more complex kinds of adaptations. There is a similar quality in human creativity. I am thinking of the aesthetic and cultural creativity of artists, but also the intellectual creativity of scientists and scholars, as well as the commercial and practical creativity of craftsmen, businessmen, and entrepreneurs. And I want to focus especially on the hyper- creative aspects of human creativity—the way in which human activity can yield qualitatively new and more complex creations. (shrink)

The field of artificial life is enriching both the content and method of philosophy. One example of the impact of artificial life on the content of philosophy is the light it sheds on the perennial philosophical question of the nature of emergent pheonomena in general. Another second example is the way it highlights and promises to explain the suppleness of mental processes. Artificial life's computational thought experiments also provide philosophy with a methodological innovation. The limitations of the central arguments in (...) Stephen Jay Gould's.. (shrink)

The new interdisciplinary science of artificial life has had a connection with the arts from its inception. This paper provides an overview of artificial life, reviews its key scientific challenges, and discusses its philosophical implications. It ends with a few words about the implications of artificial life for the arts.

Artificial life uses computer models to study the essential nature of the characteristic processes of complex adaptive systems proceses such as self-organization, adaptation, and evolution. Work in the field is guided by the working hypothesis that simple computer models can capture the essential nature of these processes. This hypothesis is illustrated by recent results with a simple population of computational agents whose sensorimotor functionality undergo open-ended adaptive evolution. These might illuminate three aspects of complex adaptive systems in general: punctuated equilibrium (...) dynamics of diversity, a transition separating genetic order and disorder, and a law of adaptive evolutionary activity. (shrink)

It’s sometimes said, and even more often assumed, that life is necessary for mind. If so, and if A-Life promises to throw light on the nature of life as such, then A-Life is in principle highly relevant to the philosophy of mind and cognitive science. However, very few philosophers have attempted to argue for the relation between life and mind. It’s usually taken for granted. Even those (mostly in the Continental tradition, including some with a following in A-Life) who have (...) insisted on the linkage have stated it rather than justified it. If an evolutionary account of intentionality is acceptable, then perhaps biological life ‘makes room’ for mind. But that claim is problematic, since it’s not clear that the type of self-organization involved in life-as-such must necessarily include evolution. Even if it does, it’s a further step to show that life is strictly necessary for mind. (shrink)

The first part of this paper explores the general issues in using Artificial Life techniques to program actual mobile robots. In particular it explores the difficulties inherent in transferring programs evolved in a simulated environment to run on an actual robot. It examines the dual evolution of organism morphology and nervous systems in biology. It proposes techniques to capture some of the search space pruning that dual evolution offers in the domain of robot programming. It explores the relationship between robot (...) morphology and program structure, and techniques for capturing regularities across this mapping. (shrink)

This paper explores how an evolutionary process can produce systems that learn. A general framework for the evolution of learning is outlined, and is applied to the task of evolving mechanisms suitable for supervised learning in single-layer neural networks. Dynamic properties of a network’s information-processing capacity are encoded genetically, and these properties are subjected to selective pressure based on their success in producing adaptive behavior in diverse environments. As a result of selection and genetic recombination, various successful learning mechanisms evolve, (...) including the well-known delta rule. The effect of environmental diversity on the evolution of learning is investigated, and the role of different kinds of emergent phenomena in genetic and connectionist systems is discussed. (shrink)

We could have been characters in a huge computer simulation. It is a familiar idea that the whole world might be simulated on a computer, and things would seem exactly the same to us (and indeed, who is to say that we are not).

The idea that biorobots can be used as a testbed for the evaluation of hypotheses about how an animal functions is supported. Generation of realistic feedback is a major advantage of biorobotic models. Nevertheless, skeptics can only be convinced that this approach is valid if significant biological insights are generated from its application.

There are two likely paths for philosophers to follow in their encounters with Artificial Life: they can see it as a new way of doing philosophy, or simply as a new object worthy of philosophical attention using traditional methods. Is Artificial Life best seen as a new philosophical method or a new phenomenon? There is a case to be made for each alternative, but I urge philosophers to take the leap and consider the first to be the more important and (...) promising. (shrink)

Is life a property of the material structure of a living system or an abstract form of organization that can be realized in other media; artificial as well as natural? One version of the Artificial Life research programme presumes, that one can separate the logical form of an organism from its material basis of construction, and that its capacity to live and reproduce is a property of the form, not the matter (Langton 1989). This seems to oppose the notion of (...) a cell within contemporary molecular biology, according to which "form" and "matter" do not represent separate realms. The information in a living cell is intimately bound to the properties of the material substrate. This condition may represent a restriction on the validity of formal theories of life. (shrink)

It is argued, that theory sf signs, especially in the tradition of the great philosopher Charles Sanders Peirce (1839–1914) can inspire the study of central problems in the philosophy of biology. Three such problems are considered: (1) The nature of biology as a science, where a semiotically informed pluralistic approach to the theory of science is introduced. (2) The peculiarity of the general object of biology, where a realistic interpretation of sign- and information-concepts is required to see sign-processes as immanent (...) in nature. (3) The possibility of an artificial construction of life, hereby discussed as a conceptual problem in the present form of the artificial life project and its implied definition of life. (shrink)

The invention of the computer has revolutionized science. With respect to finding the essential structures of life, for example, it has enabled scientists not only to investigate empirical examples, but also to create and study novel hypothetical variations by means of simulation: ‘life as it could be’. We argue that this kind of research in the field of artificial life, namely the specification, implementation and evaluation of artificial systems, is akin to Husserl’s method of free imaginative variation as applied to (...) the specific regional ontology of biology. Thus, at a time when the clarification of the essence of our biological embodiment is of growing interest for phenomenology, we suggest that artificial life should be seen as a method of externalizing some of the insurmountable complexity of imaginatively varying the phenomenon of life. (shrink)

Both Artificial Life and Artificial Mind are branches of what Dennett has called "reverse engineering": Ordinary engineering attempts to build systems to meet certain functional specifications, reverse bioengineering attempts to understand how systems that have already been built by the Blind Watchmaker work. Computational modelling (virtual life) can capture the formal principles of life, perhaps predict and explain it completely, but it can no more be alive than a virtual forest fire can be hot. In itself, a computational model is (...) just an ungrounded symbol system; no matter how closely it matches the properties of what is being modelled, it matches them only formally, with the mediation of an interpretation. Synthetic life is not open to this objection, but it is still an open question how close a functional equivalence is needed in order to capture life. Close enough to fool the Blind Watchmaker is probably close enough, but would that require molecular indistinguishability, and if so, do we really need to go that far? (shrink)

Artificial life can take two forms: synthetic and virtual. In principle, the materials and properties of synthetic living systems could differ radically from those of natural living systems yet still resemble them enough to be really alive if they are grounded in the relevant causal interactions with the real world. Virtual (purely computational) "living" systems, in contrast, are just ungrounded symbol systems that are systematically interpretable as if they were alive; in reality they are no more alive than a virtual (...) furnace is hot. Virtual systems are better viewed as "symbolic oracles" that can be used (interpreted) to predict and explain real systems, but not to instantiate them. The vitalistic overinterpretation of virtual life is related to the animistic overinterpretation of virtual minds and is probably based on an implicit (and possibly erroneous) intuition that living things have actual or potential mental lives. (shrink)

Artificial life (ALife) is the attempt to create artificial instances of life in a variety of media, but primarily within the digital computer. As such, the field brings together computationally-minded biologists and biologically-minded computer scientists. I argue that this new field is filled with interesting philosophical issues. However, there is a dearth of philosophers actively conducting research in this area. I discuss two books on the new field: Margaret A. Boden's The philosophy of artificial life and Christopher G. Langton's Artificial (...) life: an overview. They cover three areas of philosophical interest: the definition of life, the relationship between life and mind, and the possibility of creating life within a computational environment. This discussion allows me to critique past work in the philosophy of ALife that tends to see the field as a proving ground for traditional arguments from the philosophy of artificial intelligence. Instead, I suggest, what is interesting about ALife is how it differs from artificial intelligence and that the most interesting philosophical issues in the area are those derived from biology, not psychology. I recommend that these two books taken together constitute an interesting introduction to ALife and the wealth of philosophical issues found therein. (shrink)

Cyberfeminism and Artificial Life examines construction, manipulation and re-definition of life in contemporary technoscientific culture. It takes a critical political view of the concept of life as information, tracing this through the new biology and the changing discipline of artificial life and its manifestation in art, language, literature, commerce and entertainment. From cloning to computer games, and incorporating an analysis of hardware, software and 'wetware', Sarah Kember demonstrates how this relatively marginal field connects with, and connects up global networks of (...) information systems. As well as offering suggestions for the evolution of [cyber]feminism in Alife environments, the author identifies the emergence of posthumanism; an ethics of the posthuman subject mobilized in the tension between cold war and post-cold war politics, psychological and biological machines, centralized and de-centralized control, top-down and bottom-up processing, autonomous and autopoietic organisms, cloning and transgenesis, species-self and other species. Ultimately, this book aims to re-focus concern on the ethics rather than on the 'nature' of life-as-it-could-be. (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)

Inventions should belong to no one. It does not matter whether the invention is a genetically engineered life form or a mechanism such as the more familiar radio: it should not be private property. More precisely, types of things invented by people (such as the radio or the dog) as opposed to particular things (such as the radio in my car and the dog in my back yard) should not be private property, with one qualification: At most, people should expect (...) monopolies for brief periods of time on the use of the types of gadgets and creatures they invent, after which such types of things (again: as distinct from particular gadgets and creatures) should be freely accessible by all. The monopoly I have in mind bears some resemblance to the monopoly provided by the patent system, but towards the end of the essay I will suggest ways in which that system needs to be rethought, restructured, and extended. (shrink)

In this paper I explore the question of how artificial life might be used to get a handle on philosophical issues concerning the mind-body problem. I focus on questions concerning what the physical precursors were to the earliest evolved versions of intelligent life. I discuss how cellular automata might constitute an experimental platform for the exploration of such issues, since cellular automata offer a unified framework for the modeling of physical, biological, and psychological processes. I discuss what it would take (...) to implement in a cellular automaton the evolutionary emergence of cognition from non-cognitive artificial organisms. I review work on the artificial evolution of minimally cognitive organisms and discuss how such projects might be translated into cellular automata simulations. (shrink)

In this paper I discuss one of the key issuesin the philosophy of neuroscience:neurosemantics. The project of neurosemanticsinvolves explaining what it means for states ofneurons and neural systems to haverepresentational contents. Neurosemantics thusinvolves issues of common concern between thephilosophy of neuroscience and philosophy ofmind. I discuss a problem that arises foraccounts of representational content that Icall ``the economy problem'': the problem ofshowing that a candidate theory of mentalrepresentation can bear the work requiredwithin in the causal economy of a mind and (...) anorganism. My approach in the current paper isto explore this and other key themes inneurosemantics through the use of computermodels of neural networks embodied and evolvedin virtual organisms. The models allow for thelaying bare of the causal economies of entireyet simple artificial organisms so that therelations between the neural bases of, forinstance, representation in perception andmemory can be regarded in the context of anentire organism. On the basis of thesesimulations, I argue for an account ofneurosemantics adequate for the solution of theeconomy problem. (shrink)

Computation and philosophy intersect three times in this essay. Computation is considered as an object, as a method, and as a model used in a certain line of philosophical inquiry concerning the relation of mind to matter. As object, the question considered is whether computation and related notions of mental representation constitute the best ways to conceive of how physical systems give rise to mental properties. As method and model, the computational techniques of artificial life and embodied evolutionary connectionism are (...) used to conduct prosthetically enhanced thought experiments concerning the evolvability of mental representations. Central to this essay is a discussion of the computer simulation and evolution of three-dimensional synthetic animals with neural network controllers. The minimally cognitive behavior of finding food by exhibit- ing positive chemotaxis is simulated with swimming and walking creatures. These simulations form the basis of a discussion of the evolutionary and neurocomputa- tional bases of the incremental emergence of more complex forms of cognition. Other related work has been used to attack computational and representational theories of cognition. In contrast, I argue that the proper understanding of the evolutionary emergence of minimally cognitive behaviors is computational and representational through and through. (shrink)

This article concerns the claim that it is possible to create living organisms, not merely models that represent organisms, simply by programming computers ("virtual" strong alife). I ask what sort of things these computer-generated organisms are supposed to be (where are they, and what are they made of?). I consider four possible answers to this question: (a) The organisms are abstract complexes of pure information; (b) they are (...) material objects made of bits of computer hardware; (c) they are physical processes going on inside the computer; and (d) they are denizens of an entire artificial world, different from our own, that the programmer creates. I argue that (a) could not be right, that (c) collapses into (b), and that (d) would make strong alife either absurd or uninteresting. Thus, "virtual" strong alife amounts to the claim that, by programming a computer, one can literally bring bits of its hardware to life. (shrink)

Mirror neurons may play a role in representing not only signs but also their meaning. Because actions are the only aspect of behavior that are inter-individually accessible, interpreting meanings in terms of actions might explain how meanings can be shared. Behavioral evidence and artificial life simulations suggest that seeing objects or processing words referring to objects automatically activates motor actions.

Because evolution in natural systems happens so slowly, it is dif- ficult to design inquiry-based labs where students can experiment and observe evolution in the way they can when studying other phenomena. New research in evolutionary computation and artificial life provides a solution to this problem. This paper describes a new A-Life software environment – Avida-ED – in which undergraduate students can test evolutionary hypotheses directly using digital organisms that evolve on their own through the very mechanisms that Darwin discovered.

In this paper I provide an epistemological context for Artificial Life projects. Later on, the insights which such projects will exhibit may be used as a general direction for further Artificial Life implementations. The purpose of such a model is to demonstrate by way of simulation how higher cognitive structures may emerge from building invariants by simple sensorimotor beings. By using the bottom-up methodology of Artificial Life, it is hoped to overcome problems that arise from dealing with complex systems, such (...) as the phenomenon of cognition. The research will lead to both epistemological and technical implications.
The proposed ALife model is intended to point out the usefulness of an interdisciplinary approach including methodological approaches from disciplines such as Artificial Intelligence, Cognitive Science, Theoretical Biology, and Artificial Life. I try to put them in one single context. The epistemological background which is necessary for this purpose comes from the ideas developed in both epistemological and psychological Constructivism.
The model differs from other ALife approaches— and is somewhat radical in this sense—as it tries to start on the lowest possible level, i.e. avoids several a priori assumptions and anthropocentric ascriptions. Due to this characterization, the project may be alternatively viewed as testing the complementary relationship between epistemology and methodology. (shrink)

Since antiquity, philosophers and engineers have tried to take life’s measure by reproducing it. Aiming to reenact Creation, at least in part, these experimenters have hoped to understand the links between body and spirit, matter and mind, mechanism and consciousness. Genesis Redux examines moments from this centuries-long experimental tradition: efforts to simulate life in machinery, to synthesize life out of material parts, and to understand living beings by comparison with inanimate mechanisms. Jessica Riskin collects seventeen essays from distinguished scholars in (...) several fields. These studies offer an unexpected and far-reaching result: attempts to create artificial life have rarely been driven by an impulse to reduce life and mind to machinery. On the contrary, designers of synthetic creatures have generally assumed a role for something nonmechanical. The history of artificial life is thus also a history of theories of soul and intellect. Taking a historical approach to a modern quandary, Genesis Redux is essential reading for historians and philosophers of science and technology, scientists and engineers working in artificial life and intelligence, and anyone engaged in evaluating these world-changing projects. (shrink)

The future of ethics -- Minds and related matters -- On transition -- The colors of life -- The far future -- At the limits of the conceivable -- Loose ends and final thoughts.

We have created the homunculus and have seen the monstrous being. Forty days the sperm lay buried in manure and each day at noon the Master turned his magnet across it, muttering foreign words. Then, on the fortieth day he showed me the resemblance of a man, but it was transparent, without a corpus. He told me we should feed the loathsome object for exactly forty weeks, and all this time allow it to lie in its bed of manure in (...) a continual and even temperature, so that its every member might develop. This we did, much against my will. And it grew into a human child, though much smaller than any born of Woman. Now, my friends ask me to make one for them That they may be as horrified as I. I would do so for their admiration, except that I am merely the apprentice of the Master, and I am afraid. (shrink)

Pioneer approaches to Artificial Intelligence have traditionally neglected, in a chronological sequence, the agent body, the world where the agent is situated, and the other agents. With the advent of Collective Robotics approaches, important progresses were made toward embodying and situating the agents, together with the introduction of collective intelligence. However, the currently used models of social environments are still rather poor, jeopardizing the attempts of developing truly intelligent robot teams. In this paper, we propose a roadmap for a new (...) approach to the design of multi-robot systems, mainly inspired by concepts from Institutional Economics, an alternative to mainstream neoclassical economic theory. Our approach intends to sophisticate the design of robot collectives by adding, to the currently popular emergentist view, the concepts of physically and socially bounded autonomy of cognitive agents, uncoupled interaction among them and deliberately set up coordination devices. (shrink)

This volume is the direct result of a conference in which a number of leading researchers from the fields of artificial intelligence and biology gathered to ...

Artificial Life (ALife) has two goals. One attempts to describe fundamental qualities of living systems through agent based computer models. And the second studies whether or not we can artificially create living things in computational mediums that can be realized either, virtually in software, or through biotechnology. The study of ALife has recently branched into two further subdivisions, one is “dry” ALife, which is the study of living systems “in silico” through the use of computer simulations, and the other is (...) “wet” ALife that uses biological material to realize what has only been simulated on computers, effectively wet ALife uses biological material as a kind of computer. This is challenging to the field of computer ethics as it points towards a future in which computer and bioethics might have shared concerns. The emerging studies into wet ALife are likely to provide strong empirical evidence for ALife’s most challenging hypothesis: that life is a certain set of computable functions that can be duplicated in any medium. I believe this will propel ALife into the midst of the mother of all cultural battles that has been gathering around the emergence of biotechnology. Philosophers need to pay close attention to this debate and can serve a vital role in clarifying and resolving the dispute. But even if ALife is merely a computer modeling technique that sheds light on living systems, it still has a number of significant ethical implications such as its use in the modeling of moral and ethical systems, as well as in the creation of artificial moral agents. (shrink)

What is artificial life? Much has been said about this interesting collection of efforts to artificially simulate and synthesize lifelike behavior and processes, yet we are far from having a robust philosophical understanding of just what Alifers are doing and why it ought to interest philosophers of science, and philosophers of biology in particular. In this paper, I first provide three introductory examples from the particular subset of artificial life I focus on, known as ‘soft Alife’ (s-Alife), and follow up (...) with a more in-depth review of the Avida program, which serves as my case study of s-Alife. Next, I review three well-known accounts of thought experiments, and then offer my own synthesized account, to make the argument that s-Alife functions as thought experimentation in biology. I draw a comparison between the methodology of the thought-experimental world that yields real-world results, and the s-Alife research that informs our understanding of natural life. I conclude that the insights provided by s-Alife research have the potential to fundamentally alter our understanding of the nature of organic life and thus deserve the attention of both philosophers and natural scientists. (shrink)

We explicate representational content by addressing how representations that ex- plain intelligent behavior might be acquired through processes of Darwinian evo- lution. We present the results of computer simulations of evolved neural network controllers and discuss the similarity of the simulations to real-world examples of neural network control of animal behavior. We argue that focusing on the simplest cases of evolved intelligent behavior, in both simulated and real organisms, reveals that evolved representations must carry information about the creature’s environ- ments (...) and further can do so only if their neural states are appropriately isomor- phic to environmental states. Further, these informational and isomorphism rela- tions are what are tracked by content attributions in folk-psychological and cognitive scientific explanations of these intelligent behaviors. (shrink)

The idea that gravity affects dorso-ventral polarization in anouran development contrasts with the theories of self-organization through reaction-diffusion processes. As a result of a literature study we discuss the role of gravity in embryological axis formation and speculate on an influence of gravity on tissue compartmentalization. The involvement of compartmentalization in tissue homeostasis is discussed in the light of the recent progress in mammalian cell culture studies.

In spite of the tremendous progress in recent decades of biological science, many aspects of the behaviour of organisms in general and of humans in particular remain still somewhat obscure. A new approach towards the study of the behaviour of man was presented by Heisenberg when he emphasized that a Cartesian view of nature as an object out there is an illusion in so far as the observer is always part of the formula, the man viewing nature must be figured (...) in, the experimenter into his experiment and the artist in the scene he paints. (Heisenberg, 1969).The present study is an attempt to make a step forward in this direction by focusing on the ways and means of involvement of the observer which make him an indelible part of the observation. (shrink)

Machine generated contents note: -- 1. Quantum Mechanics as a General Framework -- 2. Classical and Quantum Information and Entropy -- 3. The Brain: An Outlook -- 4. Vision -- 5. Dealing with Target's Motion and Our Own Movement -- 6. Complexity: A Necessary Condition -- 7. General Features of Life -- 8. The Organism as a Semiotic and Cybernetic System -- 9. Phylogeny -- 10. Ontogeny -- 11. Epigeny -- 12. Representational Semiotics -- 13. The Brain as an Information-Control (...) System -- 14. Decisional, Emotional and Cognitive Systems -- 15. Behavior -- 16. Learning -- 17. Memory -- 18. The Basic Symbolic Systems -- 19. What Symbols Are -- 20. Intentionality and Conceptualization -- 21. Consciousness -- 22. Development and Culture -- 23. Language -- 24. Mind and Brain (Body) -- 25. Final Philosophical Remarks. (shrink)

National Cancer Institute, Frederick Cancer Research and Development Center, Laboratory of Experimental and Computational Biology, PO Box B, Frederick, MD 21702-1201, USA..

This paper discussses various concepts of biological information with particular attention being paid to genetic information.

Organisms inherit various kinds of developmental information and cues from their parents. The study of inheritance systems is aimed at identifying and classifying the various mechanisms and processes of heredity, the types of hereditary information that is passed on by each, the functional interaction between the different systems, and the evolutionary consequences of these properties. We present the discussion of inheritance systems in the context of several debates. First, between proponents of monism about heredity (gene-centric views), holism about heredity (Developmental (...) Systems Theory), and those stressing the role of multiple systems of inheritance. Second, between those analyzing inheritance solely in terms of replication and transmission, and views that stress the multi-generation reproduction of phenotypic traits. A third debate is concerned with different criteria that have been proposed for identifying and delimiting inheritance systems. A fourth controversy revolves around the significance of the “Lamarckian” aspects of some of the inheritance systems that have been identified, such as epigenetic inheritance and behavioral inheritance, that allow the transmission of environmentally induced characters (i.e., “soft inheritance”). (shrink)

Recent and not so recent advances in our molecular understanding of the genome make the once prevalent view of the genome as a passive container of genetic information (i.e., genes) untenable, and emphasize the importance of the internal organization and re-organization dynamics of the genome for both development and evolution. While this conclusion is by now well accepted, the construction of a comprehensive conceptual framework for studying the genome as a dynamic system, capable of self-organization and adaptive behavior is still (...) underway. This work deals with the effect of such a conceptual shift on evolutionary thought. Specifically, I try to articulate the conceptual commitments and obligations of views that privilege explanatorily or causally the genome, its dynamics and mechanisms, over genes. I refer to this class of views as belonging to ‘the genome perspective’. (shrink)

The received view in philosophy of biology is that there is a well-understood, philosophically rigorous account of information—causal information. I argue that this view is mistaken. Causal information is fatally undermined by misinterpretations and conflations between distinct independent accounts of information. As a result, philosophical arguments based on causal information are deeply flawed. I end by briefly considering what a correct application of the relevant accounts of information would look like in the biological context.

Much of the debate surrounding the concept of information in biology centers on the question of whether or not biological systems ‘really’ carry information. The criterion for determining if a system “really” carries information is whether or not there is a principled, theoretical account of information that captures the relevant biological usages. If biological systems do not carry information in this sense, information talk is termed merely heuristic and dismissed as philosophically uninteresting. To date, all three proposed theoretical accounts of (...) information—mathematical, causal and teleosemantic—fail to capture the meaning of biologists. Details of other biological practices that utilize informational concepts are often lost because the debate is too focused on one instance of information talk—genetic information and because biological representations are thought to need a certain kind of theoretical foundation. The problem with this methodology is that it takes the failure of philosophical accounts of information to capture current biological practices as conclusive evidence that informational representations in biology are incoherent. This approach is backwards. A better strategy is to get a clear understanding of biological practice and then to use it to shape our understanding of the philosophical significance of biological information. In this paper, I shift attention from abstract reasoning about information in the philosophical literature to concrete reasoning about informational models in biology. The current debate pays too little attention to the biologically prominent concept of signal. I develop a contextualized understanding of signaling models in biological practice. I argue that biologists use the concept of signal to model distinct functional roles in biological systems and not in any of the theoretical senses of information found in the current philosophical literature. For cell biologists, a signal causally indicates the state of a system at a given point and is used in the context of a style of functional explanation generally known as ‘causal role function,’ in which a mechanism or entity has a function if its behavior explains a contribution to a capacity of interest. I support this analysis with an example drawn from cell biology and reframe the debate over the significance of informational terms in biology. The focus on signal recasts the debate by highlighting examples of information talk which are central to active research programs in biology. The advantage of looking at these models is that their centrality to biological practice forces us to reconsider the adequacy of a methodology that dismisses biological models because we lack a particular kind of philosophical understanding of them. Standard philosophical accounts of information rely on assumptions appropriate for the needs of philosophers but are ill-suited for capturing biological practice. A contextualized understanding of the role of signal in biological practice allows us to work out from the details of practice to tackle broader philosophical issues. On this view, the significance of information talk in biology hinges more on our understanding of how biologists represent function than on our understanding of philosophical accounts of information. (shrink)

The explosion of scientific results about epigenetic and other parental effects appears bewilderingly diverse. An important distinction helps to bring order to the data. Firstly, parents can detect adaptively-relevant information and transmit it to their offspring who rely on it to set a plastic phenotype adaptively. Secondly, adaptively-relevant information may be generated by a process of selection on a reliably transmitted parental effect. The distinction is particularly valuable in revealing two quite different ways in which human cultural transmission may operate.

Coordination of immune responses in the gut is a complex task. In order to fight pathogens and maintain a defined population of commensal microbes, the mucosal immune system has to coordinate information from the external (luminal) and internal (abluminal) environment and respond accordingly. Dendritic cells (DCs) are crucial cell types involved in this process as they integrate these signals and direct immunogenic or tolerogenic responses. Here, we review how various functions of DCs depend on microbial stimuli and how these stimuli (...) influence the course of immune activation. (shrink)

The immune system, to protect the body, must discriminate between the pathogenic and non-pathogenic microbes and respond to them in different ways. How the mucosal immune system manages to make this distinction is poorly understood. We suggest here that the distinction between pathogenic and non-pathogenic microbes is made by an integrated system rather than by single types of cells or single types of receptors; a systems biology approach is needed to understand immune recognition.

Genes are thought to have evolved from long-lived and multiply-interactive molecules in the early stages of the origins of life. However, at that stage there were no replicators, and the distinction between interactors and replicators did not yet apply. Nevertheless, the process of evolution that proceeded from initial autocatalytic hypercycles to full organisms was a Darwinian process of selection of favourable variants. We distinguish therefore between Neo-Darwinian evolution and the related Weismannian and Central Dogma divisions, on the one hand, and (...) the more generic category of Darwinian evolution on the other. We argue that Hull’s and Dawkins’ replicator/interactor distinction of entities is a sufficient, but not necessary, condition for Darwinian evolution to take place. We conceive the origin of genes as a separation between different types of molecules in a thermodynamic state space, and employ a notion of reproducers. (shrink)

Computer analysis of biological systems, using approaches such as metabolic control analysis is common. A typical example is a language like Herbert Sauro's SCAMP (Sauro & Fell, 1991), which allows simulations of enzyme systems, and calculation of control coefficients and elasticities. However such systems are motivated by the underlying biochemical theory and often have limitations as programming languages which mean that they can only be applied to particular classes of problems.ABPL (a biochemical programming language) extends these ideas by adding all (...) the facilities of a fully-fledged programming language, together with some of the capabilities of a modern computer algebra system. Syntactically it derives from the programming language LISP, while the underlying functionality is that of iMAP, the successor to SCAMP. (shrink)

The aim of this work is to present aggregation methods of hierarchically organized systems allowing one to replace the initial micro-system by a macro-system described by a few global variables. We also study the relations between the fast micro-dynamics and the slow macro-dynamics which can produce global properties. Emergence corresponds to a bottom-up coupling that is the result effected by a micro-level at a macro-level. As an example, we present prey-predator models with different time scales in an heterogeneous environment. A (...) fast time scale is associated to the migration process on spatial patches and a slow time scale is associated to growth and interactions between the populations. Preys must go on spatial patches where resources are located and where predators can attack them. The efficiency of the predators to catch preys is patch dependent. Perturbation methods allow us to aggregate the initial system of differential equations for the patch sub-populations into a macro-system of two differential equations governing the total population densities. We study the case of density independent and density dependent migrations. In the latter case, we show that different functional responses can emerge in the macro prey-predator model as a result of the coupling between the slow and fast systems. (shrink)

Several key areas in modeling the cardiovascular and respiratory control systems are reviewed and examples are given which reflect the research state of the art in these areas. Attention is given to the interrelated issues of data collection, experimental design, and model application including model development and analysis. Examples are given of current clinical problems which can be examined via modeling, and important issues related to model adaptation to the clinical setting.

Abstract This paper provides an account of the experimental conditions required for establishing whether correlating or causally relevant factors are constitutive components of a mechanism connecting input (start) and output (finish) conditions. I argue that two-variable experiments, where both the initial conditions and a component postulated by the mechanism are simultaneously manipulated on an independent basis, are usually required in order to differentiate between correlating or causally relevant factors and constitutively relevant ones. Based on a typical research project molecular biology, (...) a flowchart model detailing typical stages in the formulation and testing of hypotheses about mechanistic components is also developed. Content Type Journal Article Category Original paper in Philosophy of Biology Pages 1-17 DOI 10.1007/s13194-011-0045-3 Authors Tudor M. Baetu, Department of Philosophy, University of Maryland, College Park, MD, USA Journal European Journal for Philosophy of Science Online ISSN 1879-4920 Print ISSN 1879-4912. (shrink)

We show how a simple nonlinear dynamical system (the discrete quadratic iteration on the unit segment) can be the basis for modelling the embryogenesis process. Such an approach, even though being crude, can nevertheless prove to be useful when looking with the two main involved processes:i) on one hand the cell proliferation under successive divisions ii) on the other hand, the differentiation between cell lineages. We illustrate this new approach in the case of Caenorhabditis elegans by looking at the early (...) stages of embryogenesis, up to several hundreds of cells (lima bean larval stage). We show how the many results that have been obtained by several groups can be interpreted in terms of values for the parameters controlling the dynamical system. Furthermore, we can extend the model to the cases of genetic mutations. More precisely the teratogenetic and lethal effects are associated with abnormal variation of the control parameters with time. (shrink)

We used computer simulations to study the possible role of the dispersion of cellular coupling, refractoriness or both, in the mechanisms underlying cardiac arrhythmias. Local ischemia was first assumed to induce cell to cell dispersion of the coupling resistance (Case 1), refractory period (Case 2), or both of them (Case 3). Our numerical experiments based on the van Capelle and Durrer model showed that vortices could not be induced by cell to cell variations. With cellular properties dispersed in a patchy (...) way within the ischemic zone, a single activation wave could give rise to abnormal activities. This demonstrates the stability of the wave front under small inhomogeneities. Probabilities of reentry, estimated for the three cases cited above showed that a severe alteration of the coupling resistance may be an important factor in the genesis of reentry. Moreover, use of isochronal maps revealed that vortices were both stable and sustained with an alteration of the coupling alone or combined with a reduction of the action potential duration. Conversely, simulations with reduction of the refractoriness alone, inducing only transient patterns, could exhibit functionally determined reentries. (shrink)

The present work is aimed at investigating the effects of myocardial infarction and ischemia on induction of ventricular fibrillation. Electrophysiologic effects of global and local ischemia (variation of the dispersion of refractory periods as well as conduction velocity) on initiation of reentry mechanisms was studied by means of computer simulations based on a cellular automata model of propagation of activation wave through a ventricular surface element. A local area of ischemia where effects of the dispersion of refractory periods are investigated (...) is then simulated. This is made using a Gaussian distribution characterized by its mean and standard deviation. These simulations show that ischemia is capable of initiating reentry phenomena which propagate through the whole ventricle; they are responsible for ventricular fibrillation which causes sudden cardiac death, even when ischemia only involves limited parts of the myocardium. Statistical study of the probability of reentries as a function of both of the size of ischemic zones and the rate of dispersion of refractory periods shows that the latter parameter is of primary importance in triggering cardiac reentries. (shrink)

Limitations of antiarrhythmic drugs on cardiac sudden death prevention appeared since the early 80's. The "Cardiac Arrhythmia Suppression Trial"(CAST) showed more recently that mortality was significantly higher inpatients treated with some particular antiarrhythmic drugs than in non-treated patients. In this field, our group recently demonstrated that a bolus of a Class 1B antiarrhythmic drug was able to trigger a ventricular fibrillation due to transient blocks induction. The aim of the present work was to systematically study, by use of the van (...) Capelle and Durrer (VCD) model which allows to simulate ventricular activation wave propagation, the link between arrhythmogenic effects and the ability of transient blocks to possibly degenerate in severe arrhythmias. A fragment of the ventricular wall is represented by an array of 16384elements electrically coupled. Effects of induction of one or several transient blocks, as the effects of their size and duration on possible induction of reentries have been studied. Results obtained show that various combinations between these different parameters may trigger reentries, ventricular tachycardia and/or more complex patterns assimilable to ventricular fibrillation. These results clearly evidence the fact that possible induction of transient blocks may directly be related to risk factor associated to arrhythmogenic effects of antiarrhythmic drugs. (shrink)

Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecendented in its combination of biology with a ...

Historically embryogenesis has been among the most philosophically intriguing phenomena. In this paper I focus on one aspect of biological development that was particularly perplexing to the ancients: self-organisation. For many ancients, the fact that an organism determines the important features of its own development required a special model for understanding how this was possible. This was especially true for Aristotle, Alexander, and Simplicius who all looked to contemporary technology to supply that model. However, they did not all agree on (...) what kind of device should be used. In this paper I explore the way these ancients made use of technology as a model for the developing embryo. However, my purpose here is more than just the historical interest of knowing which devices were used by whom and how each of them worked; I shall largely ignore the details of how the various devices actually worked. Instead I shall look at the use of technology from a philosophical perspective. As we shall see, the different choices of device reveal fundamental differences in the way each thinker understood the nature of biological development itself. Thus, the central aim of this paper is to examine, not who used what devices and how they worked, but why they used those particular devices and what they thought their functioning could tell us about the nature of embryological phenomena. (shrink)

The concepts of adaptive/fitness landscapes and adaptive peaks are a central part of much of contemporary evolutionary biology; the concepts are introduced in introductory texts, developed in more detail in graduate-level treatments, and are used extensively in papers published in the major journals in the field. The appeal of visualizing the process of evolution in terms of the movement of populations on such landscapes is very strong; as one becomes familiar with the metaphor, one often develops the feeling that it (...) is possible to gain deep insights into evolution by thinking about the movement of populations on landscapes consisting of adaptive valleys and peaks. But, since Wright first introduced the metaphor in 1932, the metaphor has been the subject of persistent confusion, from equivocation over just what the features of the landscape are meant to represent to how we ought to expect the landscapes to look. Recent advances—conceptual, empirical, and computational—have pointed towards the inadequacy and indeed incoherence of the landscapes as usually pictured. I argue that attempts to reform the metaphor are misguided; it is time to give up the pictorial metaphor of the landscape entirely and rely instead on the results of formal modeling, however difficult such results are to understand in ‘intuitive’ terms. (shrink)

A formal theory of the ecological niche is indispensable not only for semantic precision in philosophy to understand and compare it with other meanings of niche, but also when computer scientists and ecologists desire to create interoperable software where one can retrieve the niche of a species and compare their parameters. The proposed model is a more fine-grained description of the ecological niche, including the distinction between its complex concept, the abstract niche (‘fundamental niche’) with its hypervolume in multidimensional space, (...) and its realisations (‘realised niches’). The presented ecological niche may initiate new avenues for research in ecology, particularly concerning the conditions/categories of a hypervolume, as well as further philosophical inquiry and comparison with other niches. (shrink)

This paper aims to identify the key characteristics of model organisms that make them a specific type of model within the contemporary life sciences: in particular, we argue that the term “model organism” does not apply to all organisms used for the purposes of experimental research. We explore the differences between experimental and model organisms in terms of their material and epistemic features, and argue that it is essential to distinguish between their representational scope and representational target. We also examine (...) the characteristics of the communities who use these two types of models, including their research goals, disciplinary affiliations, and preferred practices to show how these have contributed to the conceptualization of a model organism. We conclude that model organisms are a specific subgroup of organisms that have been standardized to fit an integrative and comparative mode of research, and that it must be clearly distinguished from the broader class of experimental organisms. In addition, we argue that model organisms are the key components of a unique and distinctively biological way of doing research using models. (shrink)

Despite their best efforts, scientists may be unable to construct models that simultaneously exemplify every theoretical virtue. One explanation for this is the existence of tradeoffs: relationships of attenuation that constrain the extent to which models can have such desirable qualities. In this paper, we characterize three types of tradeoffs theorists may confront. These characterizations are then used to examine the relationships between parameter precision and two types of generality. We show that several of these relationships exhibit tradeoffs and discuss (...) what consequences those tradeoffs have for theoretical practice. (shrink)

Coordination of immune responses in the gut is a complex task. In order to fight pathogens and maintain a defined population of commensal microbes, the mucosal immune system has to coordinate information from the external (luminal) and internal (abluminal) environment and respond accordingly. Dendritic cells (DCs) are crucial cell types involved in this process as they integrate these signals and direct immunogenic or tolerogenic responses. Here, we review how various functions of DCs depend on microbial stimuli and how these stimuli (...) influence the course of immune activation. (shrink)

Limitations of antiarrhythmic drugs on cardiac sudden death prevention appeared since the early 80's. The "Cardiac Arrhythmia Suppression Trial"(CAST) showed more recently that mortality was significantly higher inpatients treated with some particular antiarrhythmic drugs than in non-treated patients. In this field, our group recently demonstrated that a bolus of a Class 1B antiarrhythmic drug was able to trigger a ventricular fibrillation due to transient blocks induction. The aim of the present work was to systematically study, by use of the van (...) Capelle and Durrer (VCD) model which allows to simulate ventricular activation wave propagation, the link between arrhythmogenic effects and the ability of transient blocks to possibly degenerate in severe arrhythmias. A fragment of the ventricular wall is represented by an array of 16384elements electrically coupled. Effects of induction of one or several transient blocks, as the effects of their size and duration on possible induction of reentries have been studied. Results obtained show that various combinations between these different parameters may trigger reentries, ventricular tachycardia and/or more complex patterns assimilable to ventricular fibrillation. These results clearly evidence the fact that possible induction of transient blocks may directly be related to risk factor associated to arrhythmogenic effects of antiarrhythmic drugs. (shrink)

In this paper, using a multilevel approach, we defend the positive role of natural selection in the generation of organismal form. Despite the currently widespread opinion that natural selection only plays a negative role in the evolution of form, we argue, in contrast, that the Darwinian factor is a crucial (but not exclusive) factor in morphological organization. Analyzing some classic arguments, we propose incorporating the notion of ‘downward causation’ into the concept of ‘natural selection.’ In our opinion, this kind of (...) causation is fundamental to the operation of selection as a creative evolutionary process. (shrink)

We have argued elsewhere that: (A) Natural selection is not a cause of evolution. (B) A resolution-of-forces (or vector addition) model does not provide us with a proper understanding of how natural selection combines with other evolutionary influences. These propositions have come in for criticism recently, and here we clarify and defend them. We do so within the broad framework of our own “hierarchical realization model” of how evolutionary influences combine.

We have argued elsewhere that: (A) Natural selection is not a cause of evolution. (B) A resolution-of-forces (or vector addition) model does not provide us with a proper understanding of how natural selection combines with other evolutionary influences. These propositions have come in for criticism recently, and here we clarify and defend them. We do so within the broad framework of our own “hierarchical realization model” of how evolutionary influences combine.

How do fitness and natural selection relate to other evolutionary factors like architectural constraint, mode of reproduction, and drift? In one way of thinking, drawn from Newtonian dynamics, fitness is one force driving evolutionary change and added to other factors. In another, drawn from statistical thermodynamics, it is a statistical trend that manifests itself in natural selection histories. It is argued that the first model is incoherent, the second appropriate; a hierarchical realization model is proposed as a basis for a (...) statistical treatment. It emerges that natural selection does not cause evolution; it just is evolution. The theory incorporates relations of statistical correlation, but not the kind of causation found in fundamental physical processes. (shrink)

The authors attempt to show that certain forms of behavior of the human immune system are illuminatingly regarded as errors in that system's operation. Since error-ascription can occur only within the context of an intentional/teleological characterization of the system, it follows that such a characterization is illuminating. It is argued that error-ascription is objective, non-anthropomorphic, irreducible to any purely causal form of explanation of the same behavior, and further that it is wrong to regard all errors of the immune system (...) as due to malfunction or maladaptation. <br>. (shrink)