The progress of the molecular biosciences has been so enormous that a discipline studying how cellular functioning emerges out of the behaviors of their molecular constituents has become reality. Systems biology studies cells as spatiotemporal networks of interacting molecules using an integrative approach of theory , experimental biology , and quantitative network-wide analytical measurement . Its aim is to understand how molecules jointly bring about life. Systems biology is rapidly discovering principles governing the functioning of molecular networks and methods to (...) model and measure them. The application of the conceptual strength of systems sciences such as physics and engineering are opening up new ways of experimentally studying the design and functioning of molecular networks. Typically, in such studies models are used to highlight principles, design experiments, or to act in a predictive mode to specifically modify cellular behavior. In this trend article, theoretical approaches being applied in systems biology will be discussed. A number of books have recently appeared that deal with theoretical aspects of systems biology. In this article they are highlighted to facilitate the communication of systems biology to a broader audience. (shrink)

Schets van een samenwerkingsmodel zoals een neuroloog-psychiater, een psycholoog, een pastor en een verpleegkundige praktiseren in een Vlaamse kliniek.

The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.

Cancers often express hundreds of genes otherwise specific to germ cells, the germline/cancer (GC) genes. Here, we present and discuss the hypothesis that activation of a “germline program” promotes cancer cell malignancy. We do so by proposing four hallmark processes of the germline: meiosis, epigenetic plasticity, migration, and metabolic plasticity. Together, these hallmarks enable replicative immortality of germ cells as well as cancer cells. Especially meiotic genes are frequently expressed in cancer, implying that genes unique to meiosis may play a (...) role in oncogenesis. Because GC genes are not expressed in healthy somatic tissues, they form an appealing source of specific treatment targets with limited side effects besides infertility. Although it is still unclear why germ cell specific genes are so abundantly expressed in cancer, from our hypothesis it follows that the germline's reproductive program is intrinsic to cancer development. (shrink)

This classic, provocative introduction to classical metaphysical questions focuses on appreciating the problems, rather than attempting to proffer answers.

The Exchange of Words is a philosophical exploration of human testimony, specifically as a form of intersubjective understanding in which speakers communicate by making themselves accountable for the truth of what they say. This account weaves together themes from philosophy of language, moral psychology, action theory, and epistemology, for a new approach to this basic human phenomenon.

The paper argues for the centrality of believing the speaker (as distinct from believing the statement) in the epistemology of testimony, and develops a line of thought from Angus Ross which claims that in telling someone something, the kind of reason for belief that a speaker presents is of an essentially different kind from ordinary evidence. Investigating the nature of the audience's dependence on the speaker's free assurance leads to a discussion of Grice's formulation of non-natural meaning in an epistemological (...) light, concentrating on just how the recognition of the speaker's self-reflexive intention is supposed to count for his audience as a reason to believe P. This is understood as the speaker's explicitly assuming responsibility for the truth of his statement, and thereby constituting his utterance as a reason to believe. (shrink)

In this volume Rorty offers a Deweyan account of objectivity as intersubjectivity, one that drops claims about universal validity and instead focuses on utility for the purposes of a community. The sense in which the natural sciences are exemplary for inquiry is explicated in terms of the moral virtues of scientific communities rather than in terms of a special scientific method. The volume concludes with reflections on the relation of social democratic politics to philosophy.

Amsterdam University Press is a leading publisher of academic books, journals and textbooks in the Humanities and Social Sciences. Our aim is to make current research available to scholars, students, innovators, and the general public. AUP stands for scholarly excellence, global presence, and engagement with the international academic community.

Microbial systems biology has made enormous advances in relating microbial physiology to the underlying biochemistry and molecular biology. By meticulously studying model microorganisms, in particular Escherichia coli and Saccharomyces cerevisiae, increasingly comprehensive computational models predict metabolic fluxes, protein expression, and growth. The modeling rationale is that cells are constrained by a limited pool of resources that they allocate optimally to maximize fitness. As a consequence, the expression of particular proteins is at the expense of others, causing trade‐offs between cellular objectives (...) such as instantaneous growth, stress tolerance, and capacity to adapt to new environments. While current computational models are remarkably predictive for E. coli and S. cerevisiae when grown in laboratory environments, this may not hold for other growth conditions and other microorganisms. In this contribution, we therefore discuss the relationship between the instantaneous growth rate, limited resources, and long‐term fitness. We discuss uses and limitations of current computational models, in particular for rapidly changing and adverse environments, and propose to classify microbial growth strategies based on Grimes's CSR framework. (shrink)

Talkers are recognized more accurately if they are speaking the listeners’ native language rather than an unfamiliar language. This “language familiarity effect” has been shown not to depend upon comprehension and must instead involve language sound patterns. We further examine the level of sound-pattern processing involved, by comparing talker recognition in foreign languages versus two varieties of English, by English speakers of one variety, English speakers of the other variety, and non-native listeners. All listener groups performed better with native than (...) foreign speech, but no effect of language variety appeared: Native listeners discriminated talkers equally well in each, with the native variety never outdoing the other variety, and non-native listeners discriminated talkers equally poorly in each, irrespective of the variety's familiarity. The results suggest that this talker recognition effect rests not on simple familiarity, but on an abstract level of phonological processing. (shrink)

Richard Swinburne offers an original treatment of a question at the heart of epistemology: what makes a belief rational, or justified in holding? He maps the rival accounts of philosophers on epistemic justification ("internalist" and "externalist"), arguing that they are really accounts of different concepts. He distinguishes between synchronic justification (justification at a time) and diachronic justification (synchronic justification resulting from adequate investigation)--both internalist and externalist. He also argues that most kinds of justification are worth having because they are (...) indicative of truth; however, it is only justification of internalist kinds that can guide a believer's actions. Swinburne goes on to show the usefulness of the probability calculus in elucidating how empirical evidence makes beliefs probably true. (shrink)

This paper explores some aspects of the relation between different ways of achieving a consensus on the judgemental values of a group of indviduals; in particular, aggregation and deliberation. We argue firstly that the framing of an aggregation problem itself generates information that individuals are rationally obliged to take into account. And secondly that outputs of the deliberative process that this initiates is in tension with constraints on consensual values typically imposed by aggregation theory, at least when deliberation is modelled (...) as process of learning from others compatible with Bayesian updating principles. (shrink)

After more than a century of research on glycolysis, we have detailed descriptions of its molecular organization, but despite this wealth of knowledge, linking the enzyme properties to metabolic pathway behavior remains challenging. These challenges arise from multi‐layered regulation and the context and time dependence of component functions. However, when viewed as a system that functions according to the principles of supply and demand, a simplifying theoretical framework can be applied to study its regulation logic and to assess the coherence (...) of experimental interpretations. These principles are universally applicable, as they emphasize the common metabolic tasks of glycolysis: the provision of free‐energy carriers, and precursors for biosynthesis and stress‐related compounds. Here we will review the regulation of multi‐tasking by glycolysis and consider how an understanding of this central metabolic pathway can be pursued using general principles, rather than focusing on the biochemical details of constituent components. (shrink)

Atheism is a familiar kind of skepticism about religion. Moral error theory is an analogous kind of skepticism about morality, though less well known outside academic circles. Both kinds of skeptic face a "what next?" question: If we have decided that the subject matter (religion/morality) is mistaken, then what should we do with this way of talking and thinking? The natural assumption is that we should abolish the mistaken topic, just as we previously eliminated talk of, say, bodily humors and (...) unicorns. The fictionalist, however, offers a less obvious recommendation. According to the fictionalist, engaging in the topic in question provides pragmatic benefits that do not depend on its truth-in a way roughly analogous to engaging with a novel or a movie. The religious fictionalist maintains that even if we were atheists, we should carry on talking, thinking, and acting as if religion were true. The moral fictionalist maintains a similar view regarding moral talk, thought, and action. Both forms of fictionalism face serious challenges. Some challenges can be levelled at either form of fictionalism (or at any form of fictionalism), whereas others are problems unique to moral fictionalism or to religious fictionalism. There are important questions to be asked about the relationship between these two kinds of fictionalism. Could moral fictionalism be plausible even if religious fictionalism is not (or vice versa)? This is a volume of thirteen previously unpublished papers on the topics of religious fictionalism, moral fictionalism, and the relation between these views. (shrink)

This book brings together twenty articles giving a comprehensive view of the work of the Aristotelian commentators.... The importance of the commentators is partly that they represent the thought and classroom teaching of the Aristotelian and Neoplatonist schools and partly that they provide a panorama of a thousand years of anicient Greek philosophy, revealing many original quotations from lost works. Even more significant is the profound influence... that they exert on later philosophy, Islamic and Western. Not only did they preserve (...) anti-Aristotelian marterial which helped inspire Medieval and Renaissance science, but they presented Aristotle in a form that made him acceptable to the Christian Church. It is not Aristotle, but Aristotle transformed and embedded in the philosophy of the commentators, that so often lies behind the views of later thinkers. --From book jacket. (shrink)

We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad's classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...) within the system cannot be predicted, even in principle, from the behavior of the system's parts within simpler wholes then there also will be systemic properties which cannot be predicted, even in principle, on basis of the behavior of these parts. We show in an explicit case study drawn from molecular cell physiology that biochemical networks display this kind of emergence, even though they deploy only mechanistic explanations. This illustrates emergence and its place in nature. (shrink)

In his final work, Richard Rorty provides the definitive statement of his political thought. Rorty equates pragmatism with anti-authoritarianism, arguing that because there is no authority we can rely on to ascertain truth, we can only do so intersubjectively. It follows that we must learn to think and care about what others think and care about.

Richard Swinburne presents a powerful new case for substance dualism and for libertarian free will. He argues that pure mental events are distinct from physical events and interact with them, and claims that no result from neuroscience or any other science could show that interaction does not take place. Swinburne goes on to argue for agent causation, and claims that it is we, and not our intentions, that cause our brain events. It is metaphysically possible that each of us (...) could acquire a new brain or continue to exist without a brain; and so we are essentially souls. Brain events and conscious events are so different from each other that it would not be possible to establish a scientific theory which would predict what each of us would do in situations of moral conflict. Hence, we should believe that things are as they seem to be: that we make choices independently of the causes which influence us. It follows that we are morally responsible for our actions. (shrink)

Philosophy and literature enjoy a close, complex relationship. Elucidating the connections between these two fields, this book examines the ways philosophy deploys literary means to advance its practice, particularly as a way of life that extends beyond literary forms and words into physical deeds, nonlinguistic expression, and subjective moods and feelings.

_Heidegger_ is a classic introduction to Heidegger's notoriously difficult work. Truly accessible, it combines clarity of exposition with an authoritative handling of the subject-matter. Richard Polt has written a work that will become the standard text for students looking to understand one of the century's greatest minds.

We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad’s classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...) within the system cannot be predicted, even in principle, from the behavior of the system’s parts within simpler wholes then there also will be systemic properties which cannot be predicted, even in principle, on basis of the behavior of these parts. We show in an explicit case study drawn from molecular cell physiology that biochemical networks display this kind of emergence, even though they deploy only mechanistic explanations. This illustrates emergence and its place in nature. (shrink)

Richard Kilvington (ca. 1302-1361) was one of the most original and influential thinkers among the Oxford Calculators. His impact on late medieval philosophy and theology remains unquestionable. His physical, logical, and ethical solutions were extensively debated and referred to, paving the way for new approaches in philosophy and theology. This volume presents a critical edition of question 4 from Kilvington's Quaestiones super libros Sententiarum, complete with an introduction to the edition and a guide to Kilvington's theological concepts.

The sixteen essays in this volume confront the current debate about the relationship between philosophy and its history. On the one hand intellectual historians commonly accuse philosophers of writing bad - anachronistic - history of philosophy, and on the other, philosophers have accused intellectual historians of writing bad - antiquarian - history of philosophy. The essays here address this controversy and ask what purpose the history of philosophy should serve. Part I contains more purely theoretical and methodological discussion, of such (...) questions as whether there are 'timeless' philosophical problems, whether the issues of one epoch are commensurable with those of another, and what style is appropriate to the historiography of the subject. The essays in Part II consider a number of case-histories. They present important revisionist scholarship and original contributions on topics drawn from ancient, early modern and more recent philosophy. All the essays have been specially commissioned, and the contributors include many of the leading figures in the field. The volume as a whole will be of vital interest to everyone concerned with the study of philosophy and of its history. (shrink)

Thinking through the body: educating for the humanities -- The body as background -- Self-knowledge and its discontents: from Socrates to somaesthetics -- Muscle memory and the somaesthetic pathologies of everyday life -- Somaesthetics in the philosophy classroom: a practical approach -- Somaesthetics and the limits of aesthetics -- Somaesthetics and Burke's sublime -- Pragmatism and cultural politics: from textualism to somaesthetics -- Body consciousness and performance -- Somaesthetics and architecture: a critical option -- Photography as performative process -- Asian (...) ars erotica and the question of sexual aesthetics -- Philosophy as awakened life : everyday aesthetics of embodiment in American transcendentalism and Japanese Zen practice -- Somatic style. (shrink)

This Element, written for researchers and students in philosophy and the behavioral sciences, reviews and critically assesses extant work on number concepts in developmental psychology and cognitive science. It has four main aims. First, it characterizes the core commitments of mainstream number cognition research, including the commitment to representationalism, the hypothesis that there exist certain number-specific cognitive systems, and the key milestones in the development of number cognition. Second, it provides a taxonomy of influential views within mainstream number cognition research, (...) along with the central challenges these views face. Third, it identifies and critically assesses a series of core philosophical assumptions often adopted by number cognition researchers. Finally, the Element articulates and defends a novel version of pluralism about number concepts. (shrink)

Disagreement is common: even informed, intelligent, and generally reasonable people often come to different conclusions when confronted with what seems to be the same evidence. Can the competing conclusions be reasonable? If not, what can we reasonably think about the situation? This volume examines the epistemology of disagreement. Philosophical questions about disagreement arise in various areas, notably politics, ethics, aesthetics, and the philosophy of religion: but this will be the first book focusing on the general epistemic issues arising from informed (...) disagreement. Ten leading philosophers offer specially written essays which together will offer a starting-point for future work on this topic. (shrink)

Our existence is increasingly lived at a distance. As we move from flesh to image, we are in danger of losing touch with each other and ourselves. How can we combine the physical with the virtual, our embodied experience with our global connectivity? How can we come back to our senses? Richard Kearney offers a timely call for the cultivation of the basic human need to touch and be touched. He argues that touch is our most primordial sense, foundational (...) to our individual and common selves. Kearney explores the role of touch, from ancient wisdom traditions to modern therapies. He demonstrates that a fundamental aspect of touch is interdependence, its inherently reciprocal nature, which offers a crucial corrective to our fixation with control. Making the case for the complementarity of touch and technology, this book is a passionate plea to recover a tangible sense of community and the joys of life with others. (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 ...

Richard Kilvington s commentary on Aristotle s Nicomachean Ethics (14th century) offers a unique perspective of argumentation by applying concepts and terminology from the fields of logic and physics to ethical dilemmas.".

The assent of man, Michael Berube -- Getting rid of the appearance-reality distinction -- Universalist grandeur and analytic philosophy -- Romanticism, narrative philosophy, and human finitude.

The more than 40 readings in this anthology cover the most important developments of the past six decades, charting the rise and decline of logical positivism ...

Frege famously held that numbers play the role of objects in our language and thought, and that this role is on display when we use sentences like "The number of Jupiter's moons is four". I argue that this role is an example of a general pattern that also encompasses persons, times, locations, reasons, causes, and ways of appearing or acting. These things are 'objects' simply in the sense that they are answers to questions: they are the sort of thing we (...) search for and specify during investigation or inquiry. I support this epistemological conception of objects by studying specificational sentences, a class of sentences which includes Frege's original example. I defend an analysis of such sentences as question-answer pairs, and show how to formally represent this analysis using game-theoretical semantics. (shrink)

The design of new constitutions is fraught with challenges on both issues of structural design and individual rights. As both a descriptive and normative matter it is exceedingly difficult to believe that one structural solution will fit all cases. The high variation in nation size, economic development, and ethnic division can easily tilt the balance for or against a Presidential or Parliamentary system, and even within these two broad classes the differences in constitutional structure are both large and hard to (...) measure. The only confident claim is that some system of separation of powers coupled with checks and balances is needed. Deciding which system, however, is far harder. In contrast, that same level of doubt does not arise in connection with the correct specification of individual right. Strong systems of negative rights on matters of liberty, property, religion, and speech are preferable across a wide range of social organizations. On the other hand, any effort to create systems of positive entitlements will fail because of the negative effects that they have on wealth creation and the inability to define or limit the scope of the relevant entitlements. (shrink)