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)

An Internet persona known as "Erik" reviewed those aspects of my book No Free Lunch dealing with the Law of Conservation of Information and specificational resources. Erik's review is titled "On Dembski's Law of Conservation of Information" and is available at http://www.talkreason.org/articles/dembski_LCI.pdf. I respond to the review here.

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.

Richard Dawkins has popularized an argument which, according to him, proves that there is almost certainly no God. It rests on the assumption that complex and statistically improbable things are more difficult to explain than those that are not, and that any explanatory mechanism that is called on to do the explaining must show how this complexity can be built up from simpler means as it would be useless otherwise. In this paper, I first question what justifies the consideration of (...) the designer’s own complexity. I suggest a different understanding of both order and simplicity inevitable when one considers the psychological counterpart of information. I then assess what seems to be the inference engine of the proposal, the metaphor of biological organisms as either self-programmed machines or algorithms. I show how self-generated organized complexity would not sit well with our knowledge of both abduction and the theorems of information theory applied to genetics. I then turn to the positive side of Dawkins’ challenge, and I review some philosophers and their proposals for how the complexity of the world could be controlled from outside if one wanted to uphold a traditional understanding of God’s simplicity. (shrink)

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.

The New Thinking contained in this volume rejects an Evolutionary Psychology that is committed to innate domain-specific psychological mechanisms: gene-based adaptations that are unlearnt, developmentally fixed and culturally universal. But the New Thinking does not simply deny the importance of innate psychological traits. The problem runs deeper: the concept of innateness is not suited to distinguishing between the two positions. That points to a more serious problem with the concept of innateness as it is applied to human psychological phenotypes. This (...) paper argues that the features of recent human evolution highlighted by the New Thinking imply that the concept of inherited representation, set out here, is a better tool for theorising about human cognitive evolution. (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)

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)