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)

Possible effects of interaction (cross-talk) between signaling pathways is studied in a system of Reaction–Diffusion (RD) equations. Furthermore, the relevance of spontaneous neurite symmetry breaking and Turing instability has been examined through numerical simulations. The interaction between Retinoic Acid (RA) and Notch signaling pathways is considered as a perturbation to RD system of axon-forming potential for N2a neuroblastoma cells. The present work suggests that large increases to the level of RA–Notch interaction can possibly have substantial impacts on neurite outgrowth and (...) on the process of axon formation. This can be observed by the numerical study of the homogeneous system showing that in the absence of RA–Notch interaction the unperturbed homogeneous system may exhibit different saddle-node bifurcations that are robust under small perturbations by low levels of RA–Notch interactions, while large increases in the level of RA–Notch interaction result in a number of transitions of saddle-node bifurcations into Hopf bifurcations. It is speculated that near a Hopf bifurcation, the regulations between the positive and negative feedbacks change in such a way that spontaneous symmetry breaking takes place only when transport of activated Notch protein takes place at a faster rate. (shrink)

The genetic code appeared on Earth with the first cells. The codes of cultural evolution arrived almost four billion years later. These are the only codes that are recognized by modern biology. In this book, however, Marcello Barbieri explains that there are many more organic codes in nature, and their appearance not only took place throughout the history of life but marked the major steps of that history. A code establishes a correspondence between two independent 'worlds', and the codemaker is (...) a third party between those 'worlds'. Therefore the cell can be thought of as a trinity of genotype, phenotype and ribotype. The ancestral ribotypes were the agents which gave rise to the first cells. The book goes on to explain how organic codes and organic memories can be used to shed new light on the problems encountered in cell signalling, epigenesis, embryonic development, and the evolution of language. (shrink)

Many natural and biological phenomena can be depicted as networks. Theoretical and empirical analyses of networks have become prevalent. I discuss theoretical biases involved in the delineation of biological networks. The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between “program” and “data”. The evolutionary significance of the dynamics of trans-generational and inter-organism regulatory networks is explored and implications are presented for understanding the evolution of (...) the biological categories development-heredity; plasticity-evolvability; and epigenetic-genetic. (shrink)

Jaegwon Kim’s exclusion argument is a general ontological argument, applicable to any properties deemed supervenient on a microproperty basis, including biological properties. It implies that the causal power of any higher-level property must be reducible to the subset of the causal powers of its lower-level properties. Moreover, as Kim’s recent version of the argument indicates, a higher-level property can be causally efficient only to the extent of the efficiency of its micro-basis. In response, I argue that the ontology that aims (...) to capture experimentally based explanations of metabolic control systems and morphogenetic systems must involve causally relevant contextual properties. Such an ontology challenges the exclusiveness of micro-based causal efficiency that grounds Kim’s reductionism, since configurations themselves are inherently causally efficient constituents. I anticipate and respond to the reductionist’s objection that the nonreductionist ontology’s account of causes and inter-level causal relations is incoherent. I also argue that such an ontology is not open to Kim’s overdetermination objection. (shrink)

Advancing the reductionist conviction that biology must be in agreement with the assumptions of reductive physicalism (the upward hierarchy of causal powers, the upward fixing of facts concerning biological levels) A. Rosenberg argues that downward causation is ontologically incoherent and that it comes into play only when we are ignorant of the details of biological phenomena. Moreover, in his view, a careful look at relevant details of biological explanations will reveal the basic molecular level that characterizes biological systems, defined by (...) wholly physical properties, e.g., geometrical structures of molecular aggregates (cells). In response, we argue that contrary to his expectations one cannot infer reductionist assumptions even from detailed biological explanations that invoke the molecular level, as interlevel causal reciprocity is essential to these explanations. Recent very detailed explanations that concern the structure and function of chromatin—the intricacies of supposedly basic molecular level—demonstrate this. They show that what seem to be basic physical parameters extend into a more general biological context, thus rendering elusive the concepts of the basic level and causal hierarchy postulated by the reductionists. In fact, relevant phenomena are defined across levels by entangled, extended parameters. Nor can the biological context be explained away by basic physical parameters defining molecular level shaped by evolution as a physical process. Reductionists claim otherwise only because they overlook the evolutionary significance of initial conditions best defined in terms of extended biological parameters. Perhaps the reductionist assumptions (as well as assumptions that postulate any particular levels as causally fundamental) cannot be inferred from biological explanations because biology aims at manipulating organisms rather than producing explanations that meet the coherence requirements of general ontological models. Or possibly the assumptions of an ontology not based on the concept of causal powers stratified across levels can be inferred from biological explanations. The incoherence of downward causation is inevitable, given reductionist assumptions, but an ontological alternative might avoid this. We outline desiderata for the treatment of levels and properties that realize interlevel causation in such an ontology. (shrink)

The classical roots of ecological sensibility lie not only in the ?theatre of reason? (Greek nature philosophy and natural history), but also in religious mythology. More important than the world seen as the ?theatre of the gods?, however, was the radically ecological view of death stated in mythic form by Empedocles and the Pythagoreans. The very emergence of the ?theatre of reason? marked a significant stage of man's alienation from nature (and from himself), though the struggle between rationalistic anthropocentrism and (...) a more ecological perspective reappeared within philosophy itself, so that the legacy of ?the Philosopher? is a dual one. (shrink)

This paper, which is based on recent empirical research at the University of Leeds, the University of Edinburgh, and the University of Bristol, presents two difficulties which arise when condensed matter physicists interact with molecular biologists: (1) the former use models which appear to be too coarse-grained, approximate and/or idealized to serve a useful scientific purpose to the latter; and (2) the latter have a rather narrower view of what counts as an experiment, particularly when it comes to computer simulations, (...) than the former. It argues that these findings are related; that computer simulations are considered to be undeserving of experimental status, by molecular biologists, precisely because of the idealizations and approximations that they involve. The complexity of biological systems is a key factor. The paper concludes by critically examining whether the new research programme of ‘systems biology’ offers a genuine alternative to the modelling strategies used by physicists. It argues that it does not. (shrink)

One of the fundamental questions of life sciences is one of whether there are genuinely random biological processes. An affirmative or negative answer to this question may have important methodological consequences. It appears that a number of biological processes are explicitly classified as random. One of them is the so-called somatic hypermutation. However, closer analysis of somatic hypermutation reveals that it is not a genuinely random process. Somatic hypermutation is called random because the exact outcome of this process is difficult (...) to predict in practice. The case of somatic hypermutation suggests that there may be no scientific evidence of a single case of ontologically random process in the biological world. (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.