"Both superb and essential... Succi, with clarity and wit, takes us from quarks and Boltzmann to soft matter - precisely the frontier of physics and life." Stuart Kauffman, MacArthur Fellow, Fellow of the Royal Society of Canada, Gold Medal Accademia Lincea We live in a world of utmost complexity, outside and within us. There are thousand of billions of billions of stars out there in the Universe, a hundred times more molecules in a glass of water, and another hundred (...) times more in our body, all working in sync to keep us alive and well. At face value, such numbers spell certain doom for our ability to make any sense at all of the world around and within us. And yet, they don't. Why, and how - this book endeavours to provide an answer to these questions with specific reference to a selected window of the physics-biology interface. The story unfolds over four main Parts. Part I provides an introduction to the main organizational principles which govern the functioning of complex systems in general, such as nonlinearity, nonlocality and ultra-dimensions. Part II deals with thermodynamics, the science of change, starting with its historical foundations laid down in the 19th century, and then moving on to its modern and still open developments in connection with biology and cosmology. Part III deals with the main character of this book, free energy, and the wondrous scenarios opened up by its merger with the modern tools of statistical physics. It also describes the basic facts about soft matter, the state of matter most relevant to biological organisms. Finally, Part IV discusses the connection between time and complexity, and its profound implications on the human condition, i.e. the one-sided nature of time and the awareness of human mortality. It concludes with a few personal considerations about the special place of emotions and humility in science. (shrink)

Given a prime p, we exhibit a Horn sentence H p which expresses "the cardinality is not p" and has size O(p 5 log p).

This paper is an empirical investigation of how Agile and Plan-based companies address teamwork. We have performed an investigation interviewing managers of 64 companies, 23 agile (hereafter defined with the term “agile companies”) and 41 non-agile (“plan-based”). The results of the study evidence a quite different approach to teamwork and team organization. Such differences are mainly in the selection of the developers and in the emphasis of the collaboration in the development teams.

Another theme of the book is compilation techniques to boost performance. The field of static analysis for logic programs is a rapidly developing field that deserves a volume on its own. Implementations of Logic Programming Systems serves as an excellent reference and may be used as a text for a course on the subject.

We introduce a reciprocity criterion for coalition formation among goal-directed agents, which we call the indecomposable do-ut-des property. It refines an older reciprocity property, called the do-ut-des or give-to-get property by considering the fact that agents prefer to form coalitions whose components cannot be formed independently. A formal description of this property is provided as well as an analysis of algorithms and their complexity. We provide an algorithm to decide whether a coalition has the desired property, and we show that (...) the problem to verify whether a single coalition satisfies the property is tractable. Moreover, we provide an algorithm to search all the sub-coalitions of a given coalition satisfying the new property. Even if this problem is not computationally tractable, we show that in several cases, also the complexity of this problem may decrease considerably. (shrink)

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns (...) describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems. (shrink)

ArgumentThis paper analyzes the public fasts of two Italian “hunger artists,” Giovanni Succi and Stefano Merlatti, in Paris in 1886, and their ability to forego eating for a long period (thirty and fifty days respectively). Some contemporary witnesses described them as clever frauds, but others considered them to be interesting physiological anomalies. Controversies about their fasts entered academic circles, but they also spread throughout the urban public at different levels. First, Succi and Merlatti steered medical debates among physicians (...) on the “scientific” explanations of the limits of human resistance to inanition, and acted as ideal mediators for doctors’ professional interests. Second, they became useful tools for science popularizers in their attempt to gain authority in drawing the boundaries between “orthodox” and “heterodox” knowledge. Finally, in the 1880s, Succi and Merlatti’s contest, the controversy around the liquids they ingested, and their scientific supervision by medical doctors, all reinforced their own professional status as itinerant fasters in a golden decade for that kind of endeavor. For all those reasons, Succi and Merlatti can be viewed as useful, epistemologically-active charlatans. (shrink)

Cet article apporte, pour la première fois, des arguments confortant l'identification de l'emporion de Pistiros, attesté épigraphiquement dans la « Grande inscription » du village de Vetren, avec le site archéologique d'époque classique et hellénistique de la région d'Adžijska Vodenica, situé à 2 km de l'endroit où l'inscription a été trouvée. Les éléments en faveur de cette identification sont les suivants : 1) la relation entre l'emplacement de l'inscription — de l'autre côté de l'ancienne « Voie diagonale » reliant Byzance (...) à Serdica, près des ruines de la station romaine de Bona Mansio — et la vocation historique de Vemporion durant le règne de Philippe II de Macédoine ; 2) la tradition antique du nom de Pistiros jusqu'à son dernier avatar : Kapisturia ; 3) l'étymologie du nom Pistiros/Bistiros, toponyme que l'on trouve près d'une vaste étendue d'eau ; 4) l'interprétation de l'hapax epaulistes comme désignant un envoyé du roi thrace qui était obligé de passer la nuit avant le défilé de Succi (aujourd'hui Porte de Trajan) avant de poursuivre son chemin vers l'Ouest le lendemain ; 5) la localisation des Emporta Belana, d'après l'inscription, au pied du versant Sud du mont Orbélos (aujourd'hui Mt Belasitza). Historiquement Xemporion de Pistiros peut être identifié avec le chorion Masteira, mentionné par Démosthène. Des données sûres le concernant nous ont été transmises par l'historien Anaximène de Lampsaque. On tente aussi, pour la première fois, de localiser le chorion Drongilon, à partir de l'ancienne forteresse de Dingion dans la moyenne vallée de l'Hébros. L'article donne enfin une interprétation nouvelle du terme Thraces tetrachoritai, qui désignerait la zone d'occupation macédonienne à l'intérieur de la Thrace, où les quatre garnisons de Philippe II (Drongilon, Kabyle, Philippopolis et Masteira) furent en butte à la révolte. Du point de vue chronologique, cette zone fut établie au moins en deux étapes : en 352/1 et 342/1 av. J.-C. (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)

In earlier work we have described how computer algebra may be used to derive composite rate laws for complete systems of equations, using the mathematical technique of Gröbner Bases (Bennett, Davenport and Sauro, 1988). Such composite rate laws may then be fitted to experimental data to yield estimates of kinetic parameters.Recently we have been investigating the practical application of this methodology to the estimation of kinetic parameters for the closed two enzyme system of aspartate aminotransferase (AAT) and malate dehydrogenase (...) (MDH) (Fisher 1990a; Fisher 1990b; Bennett and Fisher, 1990). (shrink)

Foundations for Moral Relativism consists of five self-standing, though loosely related, essays on the nature of agency and its metaethical foundations. The essays do not aspire to offer any grand theory of agency or metaethics, but only to lay out some of the foundations for such theories. These foundations portray how agency in general is constructed in the social context of a community, how moral agency in particular is constructed in the social context of a community, and how a derivative (...) relativist account of morality can be not only intellectually respectable but also plausible. In paving the way for moral relativism, Velleman clarifies popular confusions about relativism, responds to a number of traditional objections and sketches a sophisticated version of moral relativism that is meant to improve on more simplistic versions.There is much to praise in these thought provoking essays and they are highly recommended to anyone working on agency and metaethics. They are lucid, succi .. (shrink)